Re: [gmx-users] on atomtypes
Dear Justin, You see, the ligand.itp contains the HS14 information as following, 34NT1 ADP N67 -0.859 14.0067 35 HS141 ADPH1070.406 1.0080 36 HS141 ADPH1170.419 1.0080 But when I run gmx grompp -f ions.mdp -c target_solv.gro -p topol.top -o ions.tpr, it told me the "Atomtype HS14 not found". Will you please show me the way to have the issue settled? Brett At 2016-05-12 23:20:14, "Justin Lemkul" <jalem...@vt.edu> wrote: > > >On 5/12/16 11:17 AM, Brett wrote: >> Dear All, >> >> Following is the part of the atomtypes.atp for gromos54a7: >> >> O 15.99940 ; carbonyl oxygen (C=O) >>OM 15.99940 ; carboxyl oxygen (CO-) >>OA 15.99940 ; hydroxyl, sugar or ester oxygen >>OE 15.99940 ; ether or ester oxygen >>OW 15.99940 ; water oxygen >> N 14.00670 ; peptide nitrogen (N or NH) >>NT 14.00670 ; terminal nitrogen (NH2) >>NL 14.00670 ; terminal nitrogen (NH3) >>NR 14.00670 ; aromatic nitrogen >>NZ 14.00670 ; Arg NH (NH2) >>NE 14.00670 ; Arg NE (NH) >> C 12.01100 ; bare carbon >> CH0 12.0110 ; bare sp3 carbon, 4 bound heavy atoms >> CH1 13.01900 ; aliphatic or sugar CH-group >> CH2 14.02700 ; aliphatic or sugar CH2-group >> CH3 15.03500 ; aliphatic CH3-group >> CH4 16.04300 ; methane >> CH2r 14.02700 ; CH2-group in a ring >> ... >> >> If I need to insert a new type list for example HS14 with weight 1.0080, >> should the word description of the atomtype (for example, "CH2-group in a >> ring" for "CH2r 14.02700") should be accurate or just a kind of reminder >> which the gromacas will not read? >> > >It's a comment; it's not used for anything. Note that atomtypes.atp is only >read by pdb2gmx, so if this is related to your earlier post (and if it is, >it's >better to continue a thread than to start a whole new topic) then you don't >need >to be editing this file. You need to be adding parameters in ffnonbonded.itp >or >the ligand's .itp file itself. > >> In addition, the atomtypes.atp is a readonly file in >> /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/. WIll you please let me >> know how to save it after the HS14 atomtype was added? >> > >Make a local copy of the directory, acquire admin privileges, or (most simply) >add missing parameters into the ligand's .itp file. > >-Justin > >-- >== > >Justin A. Lemkul, Ph.D. >Ruth L. Kirschstein NRSA Postdoctoral Fellow > >Department of Pharmaceutical Sciences >School of Pharmacy >Health Sciences Facility II, Room 629 >University of Maryland, Baltimore >20 Penn St. >Baltimore, MD 21201 > >jalem...@outerbanks.umaryland.edu | (410) 706-7441 >http://mackerell.umaryland.edu/~jalemkul > >== >-- >Gromacs Users mailing list > >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on atomtypes
Dear All, Following is the part of the atomtypes.atp for gromos54a7: O 15.99940 ; carbonyl oxygen (C=O) OM 15.99940 ; carboxyl oxygen (CO-) OA 15.99940 ; hydroxyl, sugar or ester oxygen OE 15.99940 ; ether or ester oxygen OW 15.99940 ; water oxygen N 14.00670 ; peptide nitrogen (N or NH) NT 14.00670 ; terminal nitrogen (NH2) NL 14.00670 ; terminal nitrogen (NH3) NR 14.00670 ; aromatic nitrogen NZ 14.00670 ; Arg NH (NH2) NE 14.00670 ; Arg NE (NH) C 12.01100 ; bare carbon CH0 12.0110 ; bare sp3 carbon, 4 bound heavy atoms CH1 13.01900 ; aliphatic or sugar CH-group CH2 14.02700 ; aliphatic or sugar CH2-group CH3 15.03500 ; aliphatic CH3-group CH4 16.04300 ; methane CH2r 14.02700 ; CH2-group in a ring ... If I need to insert a new type list for example HS14 with weight 1.0080, should the word description of the atomtype (for example, "CH2-group in a ring" for "CH2r 14.02700") should be accurate or just a kind of reminder which the gromacas will not read? In addition, the atomtypes.atp is a readonly file in /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/. WIll you please let me know how to save it after the HS14 atomtype was added? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on HS14 atomtype
Dear All, By ADP with 54a7 force field, I got a ligand.itp, which contains atomtype HS14. However when I run the md by gromacs with that ligand.itp, it told me the "Atomtype HS14 not found". WIll you please tell me how to make gromacs recognize the atomtype HS14? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on "Invalid order for directive defaults"
Dear All, In http://www.gromacs.org/Documentation/Errors?highlight=errors#Invalid_order_for_directive_xxx, it writes, "In particular, "Invalid order for directive defaults" is a result of defaults being set in the topology or force field files in the inappropriate location; the [defaults] section can only appear once and must be the first directive in the topology". In the topol.top file, can I have 2 different gromacs force fields (for example 1 amber force filed for protein and 1 gromos 54a7 for the ligand)? And if can, how can we process so that "[defaults] section can only appear once and must be the first directive in the topology", which also means, how can we process so that he "[defaults] section was deleted from the second force field? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on the itp file
Dear All, In the on-line protein-ligand md tutorial, related to the drg.itp file, there is "Let's take a look at the [ atoms ] section of our JZ4 topology: [ atoms ] ; nr type resnr resid atom cgnr charge mass 1 CH3 1 JZ4 C4 10.000 15.0350 2 CH2 1 JZ4 C14 20.059 14.0270 3 CH2 1 JZ4 C13 20.060 14.0270 4 C 1 JZ4 C12 2 -0.041 12.0110 5 CR1 1 JZ4 C11 2 -0.026 12.0110 6HC 1 JZ4 H11 20.006 1.0080 7 CR1 1 JZ4 C7 2 -0.026 12.0110 8HC 1 JZ4 H7 20.006 1.0080 9 CR1 1 JZ4 C8 2 -0.026 12.0110 10HC 1 JZ4 H8 20.007 1.0080 11 CR1 1 JZ4 C9 2 -0.026 12.0110 12HC 1 JZ4 H9 20.007 1.0080 13 C 1 JZ4 C10 30.137 12.0110 14OA 1 JZ4 OAB 3 -0.172 15.9994 15 H 1 JZ4 HAB 30.035 1.0080". May I ask, for the drg.itp file, we only need contain the [ atoms ] section, all we should contain every sections of the original drg.itp file? Secondly, suppose my ligand itp was not got by the traditional gromacs forcefiled, in this situation should we modify the atom types database we got when we originally installed the gromacs to include the atom types specified for the ligand, or we can have the ligand.itp contains a section with the specific ligand atom types information supplied? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] invalid order of directive atomtypes
Dear All, Will you please tell me why I got "invalid order of directive atomtypes? Brett Part of my itp was as following, ; ADP_BwithH_ADPBfine.itp created by acpype (Rev: 401) on Thu May 5 09:25:01 2016 [atomtypes] ;name bond_type mass charge ptype sigma epsilon Amb oo 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 p5 p5 0.0 0.0 A 3.74177e-01 8.36800e-01 ; 2.10 0.2000 os os 0.0 0.0 A 3.1e-01 7.11280e-01 ; 1.68 0.1700 c3 c3 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 oh oh 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 na na 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 ca ca 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 nc nc 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 cd cd 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 nb nb 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 nh nh 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 ho ho 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. hn hn 0.0 0.0 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 h1 h1 0.0 0.0 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157 h5 h5 0.0 0.0 A 2.42146e-01 6.27600e-02 ; 1.36 0.0150 h2 h2 0.0 0.0 A 2.29317e-01 6.56888e-02 ; 1.29 0.0157 [ moleculetype ] ;namenrexcl ADPBfine3 [ atoms ] ; nr type resi res atom cgnr charge mass ; qtot bond_type 1o 1 ADP O2A1-0.947401 16.0 ; qtot -0.947 2 p5 1 ADPPA2 1.492904 30.97000 ; qtot 0.546 3o 1 ADP O1A3-0.947401 16.0 ; qtot -0.402 4 os 1 ADP O3A4-0.634601 16.0 ; qtot -1.036 5 p5 1 ADPPB5 1.367201 30.97000 ; qtot 0.331 6o 1 ADP O1B6-0.955201 16.0 ; qtot -0.624 7o 1 ADP O2B7-0.955201 16.0 ; qtot -1.580 8o 1 ADP O3B8-0.955201 16.0 ; qtot -2.535 9 os 1 ADP O5'9-0.657901 16.0 ; qtot -3.193 10 c3 1 ADP C5' 10 0.055800 12.01000 ; qtot -3.137 11 c3 1 ADP C4' 11 0.106500 12.01000 ; qtot -3.031 12 c3 1 ADP C3' 12 0.202200 12.01000 ; qtot -2.828 13 oh 1 ADP O3' 13-0.654101 16.0 ; qtot -3.482 14 c3 1 ADP C2' 14 0.067000 12.01000 ; qtot -3.415 15 oh 1 ADP O2' 15-0.613901 16.0 ; qtot -4.029 16 c3 1 ADP C1' 16 0.039400 12.01000 ; qtot -3.990 17 os 1 ADP O4' 17-0.354800 16.0 ; qtot -4.345 Par of my topl file was as following, ; Include forcefield parameters #include "amber99sb-ildn.ff/forcefield.itp" ; Include chain topologies #include "topol_Protein_chain_A.itp" #include "topol_Protein_chain_B.itp" #include "topol_Protein_chain_C.itp" #include "topol_Protein_chain_D.itp" #include "topol_Protein_chain_E.itp" #include "topol_Protein_chain_F.itp" #include "topol_Protein_chain_G.itp" #include "topol_Protein_chain_H.itp" #include "topol_Protein_chain_I.itp" #include "topol_Protein_chain_J.itp" #include "topol_Protein_chain_K.itp" #include "topol_Protein_chain_L.itp" #include "topol_Protein_chain_M.itp" #include "topol_Protein_chain_N.itp" ; Include ligand topology #include "ADPBfine.itp" ; Include water topology #include "amber99sb-ildn.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include topology for ions #include "amber99sb-ildn.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein_chain_A 1 Protein_chain_B 1 Protein_chain_C 1 Protein_chain_D 1 Protein_chain_E 1 Protein_chain_F 1 Protein_chain_G 1 Protein_chain_H 1 Protein_chain_I 1 Protein_chain_J 1 Protein_chain_K 1 Protein_chain_L 1 Protein_chain_M 1 Protein_chain_N 1 ADPBfine 1 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on editconf
Dear All, When I process the md based on the on-line lysozyme tutorial, in the gmx editconf step, it writes "No velocities found". Will you please tell me why it writes "No velocities found" and what its effect? How can we have the velocities input and displayed in the editconf step? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on atom types related to ligand
Dear All, By ACPYPE (antechamber), I got the following gro files for ADP with AMBER (GAFF) force fields: 1 ADP O2A 1 11.124 10.200 13.406 1 ADP PA 2 11.135 10.260 13.268 1 ADP O1A 3 11.011 10.309 13.198 1 ADP O3A 4 11.237 10.383 13.274 1 ADP PB 5 11.182 10.530 13.312 1 ADP O1B 6 11.142 10.599 13.184 1 ADP O2B 7 11.081 10.516 13.422 1 ADP O3B 8 11.312 10.600 13.375 1 ADP O5' 9 11.205 10.152 13.171 1 ADP C5' 10 11.133 10.037 13.127 1 ADP C4' 11 11.124 9.933 13.239 1 ADP C3' 12 11.144 9.790 13.192 1 ADP O3' 13 11.273 9.740 13.231 1 ADP C2' 14 11.030 9.711 13.255 1 ADP O2' 15 11.073 9.590 13.318 1 ADP C1' 16 10.970 9.807 13.358 1 ADP O4' 17 10.996 9.937 13.304 1 ADP N9 18 10.825 9.785 13.390 1 ADP C4 19 10.757 9.854 13.482 1 ADP C5 20 10.620 9.800 13.485 1 ADP N7 21 10.618 9.701 13.394 1 ADP C8 22 10.741 9.692 13.338 1 ADP N3 23 10.786 9.958 13.566 1 ADP C2 24 10.694 10.008 13.651 1 ADP N1 25 10.567 9.963 13.657 1 ADP C6 26 10.524 9.861 13.579 1 ADP N6 27 10.397 9.817 13.588 1 ADP HO3' 28 11.283 9.662 13.202 1 ADP HO2' 29 11.152 9.599 13.345 1 ADP HN62 30 10.342 9.854 13.643 1 ADP HN61 31 10.370 9.752 13.538 1 ADP H5'2 32 11.044 10.062 13.098 1 ADP H5'1 33 11.178 9.998 13.050 1 ADP H8 34 10.766 9.628 13.270 1 ADP H4' 35 11.196 9.958 13.300 1 ADP H3' 36 11.142 9.781 13.095 1 ADP H2' 37 10.966 9.683 13.188 1 ADP H2 38 10.720 10.081 13.709 1 ADP H1' 39 11.011 9.794 13.445 0.97060 1.01010 0.65970 Then I check the atopetypes.atp, including the atp file for amber force fields. By my lacking knowledge, in the atp files, I cannot find atom types as O2A, O3A, PA. Will you please tell me the meaning of "A" in O2A, O3A and PA? How about O5'? what is the meaning of the Apostrophe in O5'? And why there is no N9 in the atp files? I am looking forward to getting a reply from you. Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on prodrug server
Dear All, If prodrug server wrongly assign charge group for a ligand, then what should I do? For example, I have a charge group of -1 group, however prodrug server including more atoms for this charge group and make the net charge of this charge group 0 charge. Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] questions on ligand.gro and ligand.itp preparation
Dear All, Here I have 2 questions related to the ligand.gro and ligand.itp preparation for the md of protein-ligand complex. First, we have different ways to get the ligand.itp by different serves which use different electronic charge assignment methods. Is any difference for the md result for the whole protein-ligand complex if we use ligand.itp got by different charge assignment methods? Second, in the Justin on-line tutorial for the md of protein-ligand, it has the method to edit the complex.gro, for example the Justin tutorial final format was: 163ASN C 1691 0.621 -0.740 -0.126 163ASN O1 1692 0.624 -0.616 -0.140 163ASN O2 1693 0.683 -0.703 -0.011 1JZ4 C4 1 2.429 -2.412 -0.007 1JZ4 C14 2 2.392 -2.470 -0.139 1JZ4 C13 3 2.246 -2.441 -0.181 .. 5.99500 5.19182 9.66100 0.0 0.0 -2.99750 0.0 0.0 0.0 My question is, suppose we have an artificial lysozyme which contains 2 lysozyme subunit, each subunit binding one JZ4, then how do we edit the complex.gro? Does the final complex.gro change into something like? 163ASN C 1691 0.621 -0.740 -0.126 163ASN O1 1692 0.624 -0.616 -0.140 163ASN O2 1693 0.683 -0.703 -0.011 1JZ4 C4 1 2.429 -2.412 -0.007 1JZ4 C14 2 2.392 -2.470 -0.139 1JZ4 C13 3 2.246 -2.441 -0.181 2JZ4 C4 (followed by coordinates) 2JZ4 C14 (followed by coordinates) 2JZ4 C13 (followed by coordinates) 5.99500 5.19182 9.66100 0.0 0.0 -2.99750 0.0 0.0 0.0 I am looking forward to getting your reply. Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] md example for protein complex dissociation
Dear All, Will you please show me examples that with by biological significance, a protein complex dissociated into its sub-unit during the md process? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] on md of protein-ligand
Dear Justin, Then there should be multiple ligand gro files pasted onto the single protein complex gro file, right? Brett At 2016-04-20 17:45:50, "Justin Lemkul" <jalem...@vt.edu> wrote: > > >On 4/20/16 5:21 AM, Brett wrote: >> Hi Mark, >> >> >> >> I still find it was difficult to understand. After the pdb2gmx, the >> coordinates in the gro file will be significantly (including the scale of >> the value) different from the input for pdb2gmx. Suppose my protein-ligand >> contains 6 identical ligands, the ATB like servers can only produce one set >> of topology and gro files for all 6 identical ligands (with 6 different >> initial pdbs). >> >> >> Then how do we get a single gro file containing all the coordinates >> information for the 6 subunits (relatively easy for the protein part by >> pdb2gmx) and all 6 ligands (as for we can only hav 1 set of coordinates >> information containing ligand.gro for all 6 ligands)? >> > >The ligand topology should not be different for each molecule and you don't >need >multiple copies. ADP is ADP, regardless of where it is. You upload one >coordinate file, for one molecule, to ATB, get a topology, and use it. > >-Justin > >> >> Brett >> >> >> >> >> >> >> >> >> >> At 2016-04-20 16:56:09, "Mark Abraham" <mark.j.abra...@gmail.com> wrote: >>> Hi, >>> >>> The topology and the coordinates are two separate sets of infomation. You >>> already expect that lot of conformations will be consistent with the >>> topology, and explored over the simulations. The topology generating >>> servers want a structure so they can make good chemical guesses for you. >>> But later you can combine the topology with any conformation, or even use >>> the same one for multiple identical molecules. Whether the resulting model >>> later produces good results depends on the quality of the parametrisation >>> of the whole system. >>> >>> Mark >>> >>> On Wed, 20 Apr 2016 09:47 Brett <brettliu...@163.com> wrote: >>> >>>> Dear All and Justin, >>>> >>>> >>>> Suppose my protein complex contain 4 ADP, each ADP was in one subunit. >>>> Suppose we use ATB to create the ligand ADP files for md. It seems the >>>> situation is, regardless of which of the 4 ADP pdb files was submitted, ATB >>>> will only give one identical set of topology files for ADP, and it cannot >>>> distinguish from which ADP ligand ATB got the topology files for all 4 >>>> ADPs. >>>> >>>> >>>> Here it lead to the question, how does GROMCS knows the position of each >>>> ADP in the protein complex during the md process? >>>> >>>> >>>> Let us think the question from another view. We have a protein-ligand >>>> complex pdb, and the complex contains 1 subunit and 1 ligand. We got the >>>> protein topology file by pdb2gmx, and we will find in the gro file the >>>> value of the coordinates have been changed from the original pdb >>>> coordinates for the protein-ligand. The same is true for the ligand, and if >>>> we use prodrug to get the topology file for the ligand, we will find the >>>> coordinate values of the ligand have been changed in comparison with that >>>> in the ligand pdb from the protein-ligand pdb. >>>> >>>> >>>> Thus, I would like to ask, after we edited the gro files by combining the >>>> protein part coordinates and ligand part coordinates, how GROMCS keeps that >>>> once the compiled gro file was transformed back to pdb, the ligands were in >>>> the correct ligand binding pocket in the protein? >>>> >>>> I am looking forward to getting the reply from you. >>>> >>>> >>>> Brett >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> At 2016-04-19 20:13:03, "Justin Lemkul" <jalem...@vt.edu> wrote: >>>>> >>>>> >>>>> On 4/19/16 8:10 AM, Brett wrote: >>>>>> Dear All, >>>>>> >>>>>> >>>>>> It seems the external servers preparing the ligand files (antechamber >>>> for example) not only optimize the coordinates of the ligands, but it >>>
Re: [gmx-users] on md of protein-ligand
Hi Mark, I still find it was difficult to understand. After the pdb2gmx, the coordinates in the gro file will be significantly (including the scale of the value) different from the input for pdb2gmx. Suppose my protein-ligand contains 6 identical ligands, the ATB like servers can only produce one set of topology and gro files for all 6 identical ligands (with 6 different initial pdbs). Then how do we get a single gro file containing all the coordinates information for the 6 subunits (relatively easy for the protein part by pdb2gmx) and all 6 ligands (as for we can only hav 1 set of coordinates information containing ligand.gro for all 6 ligands)? Brett At 2016-04-20 16:56:09, "Mark Abraham" <mark.j.abra...@gmail.com> wrote: >Hi, > >The topology and the coordinates are two separate sets of infomation. You >already expect that lot of conformations will be consistent with the >topology, and explored over the simulations. The topology generating >servers want a structure so they can make good chemical guesses for you. >But later you can combine the topology with any conformation, or even use >the same one for multiple identical molecules. Whether the resulting model >later produces good results depends on the quality of the parametrisation >of the whole system. > >Mark > >On Wed, 20 Apr 2016 09:47 Brett <brettliu...@163.com> wrote: > >> Dear All and Justin, >> >> >> Suppose my protein complex contain 4 ADP, each ADP was in one subunit. >> Suppose we use ATB to create the ligand ADP files for md. It seems the >> situation is, regardless of which of the 4 ADP pdb files was submitted, ATB >> will only give one identical set of topology files for ADP, and it cannot >> distinguish from which ADP ligand ATB got the topology files for all 4 >> ADPs. >> >> >> Here it lead to the question, how does GROMCS knows the position of each >> ADP in the protein complex during the md process? >> >> >> Let us think the question from another view. We have a protein-ligand >> complex pdb, and the complex contains 1 subunit and 1 ligand. We got the >> protein topology file by pdb2gmx, and we will find in the gro file the >> value of the coordinates have been changed from the original pdb >> coordinates for the protein-ligand. The same is true for the ligand, and if >> we use prodrug to get the topology file for the ligand, we will find the >> coordinate values of the ligand have been changed in comparison with that >> in the ligand pdb from the protein-ligand pdb. >> >> >> Thus, I would like to ask, after we edited the gro files by combining the >> protein part coordinates and ligand part coordinates, how GROMCS keeps that >> once the compiled gro file was transformed back to pdb, the ligands were in >> the correct ligand binding pocket in the protein? >> >> I am looking forward to getting the reply from you. >> >> >> Brett >> >> >> >> >> >> >> >> >> >> >> >> At 2016-04-19 20:13:03, "Justin Lemkul" <jalem...@vt.edu> wrote: >> > >> > >> >On 4/19/16 8:10 AM, Brett wrote: >> >> Dear All, >> >> >> >> >> >> It seems the external servers preparing the ligand files (antechamber >> for example) not only optimize the coordinates of the ligands, but it >> changes the ligand from one place to another place, thus the ligand >> coordinates by the external server cannot occupy the ligand binding pocket >> in the original protein-ligand complex. >> >> >> >> >> >> I am looking forward to getting a reply from you on how to have the >> external server processed ligand find the ligand binding pocket in the >> protein-ligand complex for md. >> >> >> > >> >Topology-generating servers aren't going to "find the ligand binding >> pocket" - >> >your job is to make sure the original coordinates are preserved, as the >> previous >> >message has instructed you on how to do. >> > >> >-Justin >> > >> >> >> >> Brett >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> At 2016-04-19 19:44:23, "suniba" <sun.i...@gmail.com> wrote: >> >>> After pdb2gmx, protein topology is prepared. You prepare the ligand >> topology from an external server or parametrize it. Then you prepare >> complex.gro and include the ligan
[gmx-users] on md of protein-ligand
Dear All and Justin, Suppose my protein complex contain 4 ADP, each ADP was in one subunit. Suppose we use ATB to create the ligand ADP files for md. It seems the situation is, regardless of which of the 4 ADP pdb files was submitted, ATB will only give one identical set of topology files for ADP, and it cannot distinguish from which ADP ligand ATB got the topology files for all 4 ADPs. Here it lead to the question, how does GROMCS knows the position of each ADP in the protein complex during the md process? Let us think the question from another view. We have a protein-ligand complex pdb, and the complex contains 1 subunit and 1 ligand. We got the protein topology file by pdb2gmx, and we will find in the gro file the value of the coordinates have been changed from the original pdb coordinates for the protein-ligand. The same is true for the ligand, and if we use prodrug to get the topology file for the ligand, we will find the coordinate values of the ligand have been changed in comparison with that in the ligand pdb from the protein-ligand pdb. Thus, I would like to ask, after we edited the gro files by combining the protein part coordinates and ligand part coordinates, how GROMCS keeps that once the compiled gro file was transformed back to pdb, the ligands were in the correct ligand binding pocket in the protein? I am looking forward to getting the reply from you. Brett At 2016-04-19 20:13:03, "Justin Lemkul" <jalem...@vt.edu> wrote: > > >On 4/19/16 8:10 AM, Brett wrote: >> Dear All, >> >> >> It seems the external servers preparing the ligand files (antechamber for >> example) not only optimize the coordinates of the ligands, but it changes >> the ligand from one place to another place, thus the ligand coordinates by >> the external server cannot occupy the ligand binding pocket in the original >> protein-ligand complex. >> >> >> I am looking forward to getting a reply from you on how to have the external >> server processed ligand find the ligand binding pocket in the protein-ligand >> complex for md. >> > >Topology-generating servers aren't going to "find the ligand binding pocket" - >your job is to make sure the original coordinates are preserved, as the >previous >message has instructed you on how to do. > >-Justin > >> >> Brett >> >> >> >> >> >> >> >> >> >> >> >> At 2016-04-19 19:44:23, "suniba" <sun.i...@gmail.com> wrote: >>> After pdb2gmx, protein topology is prepared. You prepare the ligand >>> topology from an external server or parametrize it. Then you prepare >>> complex.gro and include the ligand topology manually in topol.top (topology >>> generated by pdb2gmx). And for your second question, I used ATB today and >>> realized that one should always use "original geometry" co-ordinates as >>> 'optimized geometry' will/may cause clashes with protein etc.. So, avoid >>> PRODRG server and use ATB and then download the co-ordinates and .itp of >>> original geometry. Rest process is same as mentioned in tutorial. >>> Regards >>> >>> Sent from my iPhone >>> >>>> On 19-Apr-2016, at 4:58 pm, Brett <brettliu...@163.com> wrote: >>>> >>>> Dear All, >>>> >>>> >>>> I am learning the md of protein-ligand based on the Justin on-line >>>> tutorial. My first question is, for the topology files we need to produce >>>> the protein part and ligand part separately, and the input for pdb2gmx did >>>> not contain the ligand part. After I got the ligand files, I find the >>>> coordinate of the ligands was different from the ligand pdb in the >>>> protein-complex pdb (although the rmsd between the ligand topology and the >>>> ligand in the complex was 0). Then during md process how does GROMCS know >>>> where is the position of the ligand in the complex? >>>> >>>> >>>> Correspondingly, my second question is, suppose I have a protein dimer >>>> with 2 identical subunits, 1 subunit was a cAMP binding, and 1 was apo. >>>> Then during the md process how does GROMACS know which subunit binding >>>> with the cAMP and which subunit was apo? >>>> >>>> >>>> I am looking forward to getting a reply from you. >>>> >>>> >>>> Brett >>>> -- >>>> Gromacs Users mailing list >>>> >>>> * Please search the archive at >>
Re: [gmx-users] on md of protein-ligand
Dear All, It seems the external servers preparing the ligand files (antechamber for example) not only optimize the coordinates of the ligands, but it changes the ligand from one place to another place, thus the ligand coordinates by the external server cannot occupy the ligand binding pocket in the original protein-ligand complex. I am looking forward to getting a reply from you on how to have the external server processed ligand find the ligand binding pocket in the protein-ligand complex for md. Brett At 2016-04-19 19:44:23, "suniba" <sun.i...@gmail.com> wrote: >After pdb2gmx, protein topology is prepared. You prepare the ligand topology >from an external server or parametrize it. Then you prepare complex.gro and >include the ligand topology manually in topol.top (topology generated by >pdb2gmx). And for your second question, I used ATB today and realized that one >should always use "original geometry" co-ordinates as 'optimized geometry' >will/may cause clashes with protein etc.. So, avoid PRODRG server and use ATB >and then download the co-ordinates and .itp of original geometry. Rest process >is same as mentioned in tutorial. >Regards > >Sent from my iPhone > >> On 19-Apr-2016, at 4:58 pm, Brett <brettliu...@163.com> wrote: >> >> Dear All, >> >> >> I am learning the md of protein-ligand based on the Justin on-line tutorial. >> My first question is, for the topology files we need to produce the protein >> part and ligand part separately, and the input for pdb2gmx did not contain >> the ligand part. After I got the ligand files, I find the coordinate of the >> ligands was different from the ligand pdb in the protein-complex pdb >> (although the rmsd between the ligand topology and the ligand in the complex >> was 0). Then during md process how does GROMCS know where is the position of >> the ligand in the complex? >> >> >> Correspondingly, my second question is, suppose I have a protein dimer with >> 2 identical subunits, 1 subunit was a cAMP binding, and 1 was apo. Then >> during the md process how does GROMACS know which subunit binding with the >> cAMP and which subunit was apo? >> >> >> I am looking forward to getting a reply from you. >> >> >> Brett >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >> mail to gmx-users-requ...@gromacs.org. >-- >Gromacs Users mailing list > >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on md of protein-ligand
Dear All, I am learning the md of protein-ligand based on the Justin on-line tutorial. My first question is, for the topology files we need to produce the protein part and ligand part separately, and the input for pdb2gmx did not contain the ligand part. After I got the ligand files, I find the coordinate of the ligands was different from the ligand pdb in the protein-complex pdb (although the rmsd between the ligand topology and the ligand in the complex was 0). Then during md process how does GROMCS know where is the position of the ligand in the complex? Correspondingly, my second question is, suppose I have a protein dimer with 2 identical subunits, 1 subunit was a cAMP binding, and 1 was apo. Then during the md process how does GROMACS know which subunit binding with the cAMP and which subunit was apo? I am looking forward to getting a reply from you. Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on force field for ligand
Dear All, Does GROMACS work if the force field for ligand part is GAFF force field? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] further on: very strange phenomenon for my production MD by gromacs
Dear Mark, My protein was a 6-identical subunit protein complex, initially each subunit contains a ligand. I want to see the conformational change from ligand bond to ligand free state, during this process there were reports that significant conformation change would occur First from the initial PDB with the ligands, I delete the ligands and get the apo pdb, after pdb2gmx etc, I process the energy minimization, nvt equilibration and npt equilibration, then I start the production md. During the initial 6 ns production md, there were some conformation change observed, but I do not know whether it diffuse. In addition, I do not understand what is "the envelope of the diffusion", and does diffusion leads the box from cubic to sphere? Brett At 2016-04-15 21:30:12, "Mark Abraham" <mark.j.abra...@gmail.com> wrote: >Hi, > >On Fri, Apr 15, 2016 at 3:18 PM Brett <brettliu...@163.com> wrote: > >> Dear All, >> >> By xmgrace I have checked the xmgrace, I find the spike was between >> -8.245e+06 and -8.225e+06, is the spike massive or not? >> >> >> In addition, by >> gmx trjconv -f ma_0_1.trr -s md_0_1.tpr -o 6000pswithwater.pdb --pbc >> nojump -dump 6000, >> >> >> I got the 6 ns with water pdb and I have checked the pdb (with water box), >> I find the resi 366-367 were not disconnected! >> >> >> However, by gmx editconf, the original water box was in cubic, after "gmx >> trjconv -f ma_0_1.trr -s md_0_1.tpr -o 6000pswithwater.pdb --pbc nojump >> -dump 6000", the cubic water box was replaced by a rough sphere water box >> with the protein roughly in the center. Will you please explain why the >> cubic water box was replaced by the round sphere water box? Anything wrong >> I have made? >> > >You've simulated a bunch of molecules that diffuse. What shape would you >expect for the envelope of the diffusion? How would it vary over time? > >Further, by visual check if in a production MD I did not see residue >> disconnection caused by "Periodic_Boundary_Conditions", can we guarantee no >> minor disconnection occurred during the md (or significant bond length >> variance unobservable by the naked eye with pymol) if we did not process >> the trjconv correction step? >> > >The forces produced by such a disconnection would blow everything up >immediately. Since it didn't... > >Mark > > >> I am looking forward to getting a reply from you. >> >> >> Brett >> >> >> >> >> >> >> At 2016-04-14 20:02:43, "Mark Abraham" <mark.j.abra...@gmail.com> wrote: >> >Hi, >> > >> >If this "separation" was real, would you have expected to see >> > >> >a) a massive spike in the potential energy >> >b) complete inability for the constraint algorithm to enforce bond >> lengths? >> > >> >Hint, you haven't seen that. >> > >> >Mark >> > >> >On Thu, Apr 14, 2016 at 11:52 AM Justin Lemkul <jalem...@vt.edu> wrote: >> > >> >> >> >> >> >> On 4/14/16 5:35 AM, Brett wrote: >> >> > Dear All, >> >> > >> >> > >> >> > >> >> > Thanks the reply. >> >> > >> >> > >> >> > But I think I need to discuss with you further on whether I need to >> >> discontinue my production MD. As I mentioned, resi 366-367 separated >> from >> >> the major body of the protein. By pymol I find resi 366-367 were at one >> >> edge of the box and were almost outside of the water box, and its >> >> neighbouring residues resi 365 and resi 368 were at the opposite edge of >> >> the box and were also almost outside of the water box. >> >> > >> >> > >> >> > It seems that way, although at the initial step by editconf I have put >> >> the protein in the center of the cubic box (1.5 nm), during the first 6 >> ns >> >> the protein has moved significantly in the box, and at some moment resi >> >> 366-367 have moved out of the box, leading to the disconnection of resi >> >> 366-367 from the major body of the protein and finally leading to resi >> >> 366-367 at the opposite of its neighbouring residues resi 365 and resi >> 368 >> >> in the cubix box. >> >> > >> >> > >> >> > Am I right? >> >> > >> >> >> >> Diffusion is normal. The residues are not actually disconnected. You >
[gmx-users] further on: very strange phenomenon for my production MD by gromacs
Dear All, By xmgrace I have checked the xmgrace, I find the spike was between -8.245e+06 and -8.225e+06, is the spike massive or not? In addition, by gmx trjconv -f ma_0_1.trr -s md_0_1.tpr -o 6000pswithwater.pdb --pbc nojump -dump 6000, I got the 6 ns with water pdb and I have checked the pdb (with water box), I find the resi 366-367 were not disconnected! However, by gmx editconf, the original water box was in cubic, after "gmx trjconv -f ma_0_1.trr -s md_0_1.tpr -o 6000pswithwater.pdb --pbc nojump -dump 6000", the cubic water box was replaced by a rough sphere water box with the protein roughly in the center. Will you please explain why the cubic water box was replaced by the round sphere water box? Anything wrong I have made? Further, by visual check if in a production MD I did not see residue disconnection caused by "Periodic_Boundary_Conditions", can we guarantee no minor disconnection occurred during the md (or significant bond length variance unobservable by the naked eye with pymol) if we did not process the trjconv correction step? I am looking forward to getting a reply from you. Brett At 2016-04-14 20:02:43, "Mark Abraham" <mark.j.abra...@gmail.com> wrote: >Hi, > >If this "separation" was real, would you have expected to see > >a) a massive spike in the potential energy >b) complete inability for the constraint algorithm to enforce bond lengths? > >Hint, you haven't seen that. > >Mark > >On Thu, Apr 14, 2016 at 11:52 AM Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 4/14/16 5:35 AM, Brett wrote: >> > Dear All, >> > >> > >> > >> > Thanks the reply. >> > >> > >> > But I think I need to discuss with you further on whether I need to >> discontinue my production MD. As I mentioned, resi 366-367 separated from >> the major body of the protein. By pymol I find resi 366-367 were at one >> edge of the box and were almost outside of the water box, and its >> neighbouring residues resi 365 and resi 368 were at the opposite edge of >> the box and were also almost outside of the water box. >> > >> > >> > It seems that way, although at the initial step by editconf I have put >> the protein in the center of the cubic box (1.5 nm), during the first 6 ns >> the protein has moved significantly in the box, and at some moment resi >> 366-367 have moved out of the box, leading to the disconnection of resi >> 366-367 from the major body of the protein and finally leading to resi >> 366-367 at the opposite of its neighbouring residues resi 365 and resi 368 >> in the cubix box. >> > >> > >> > Am I right? >> > >> >> Diffusion is normal. The residues are not actually disconnected. You can >> use >> trjconv to "fix" this state, but there is nothing physically wrong with it. >> mdrun cares about physics, not our visualization convenience. >> >> -Justin >> >> > >> > Brett >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > At 2016-04-14 16:31:20, "Mark Abraham" <mark.j.abra...@gmail.com> wrote: >> >> Hi, >> >> >> >> As the link Justin gave you says, and Tsjerk has since confirmed, this >> is >> >> normal. There are infinitely many equivalent representations of your >> >> simulation, not all of which will look connected for the thing that is >> of >> >> interest. >> >> >> >> Strategies for handling visualisation are also on that link, but you >> don't >> >> need to handle anything within the simulation. >> >> >> >> Mark >> >> >> >> On Thu, 14 Apr 2016 09:48 Brett <brettliu...@163.com> wrote: >> >> >> >>> Dear All, >> >>> >> >>> As I have introduced in my previous e-mail, >> >>> >> >>> "After energy minimization and equilibrations, I am now running a 50 ns >> >>> production MD, for a protein of 6 identical subunits, with each subunit >> >>> about 300 residues (from resi 120 to resi 420), and there were no >> breaks in >> >>> any chain. Every day it runs about 1 ns, and every day I use the >> command >> >>> trjconv to get a new PDB based on the md_0_1.trr file, for the >> comparison >> >>> between the new pdb and the initial pdb. >> >>> >> >>> >> >>> Today I got the PDB at 6 ns. However when I checked i
[gmx-users] very strange phenomenon for my production MD by gromacs
Dear All, Thanks the reply. But I think I need to discuss with you further on whether I need to discontinue my production MD. As I mentioned, resi 366-367 separated from the major body of the protein. By pymol I find resi 366-367 were at one edge of the box and were almost outside of the water box, and its neighbouring residues resi 365 and resi 368 were at the opposite edge of the box and were also almost outside of the water box. It seems that way, although at the initial step by editconf I have put the protein in the center of the cubic box (1.5 nm), during the first 6 ns the protein has moved significantly in the box, and at some moment resi 366-367 have moved out of the box, leading to the disconnection of resi 366-367 from the major body of the protein and finally leading to resi 366-367 at the opposite of its neighbouring residues resi 365 and resi 368 in the cubix box. Am I right? Brett At 2016-04-14 16:31:20, "Mark Abraham" <mark.j.abra...@gmail.com> wrote: >Hi, > >As the link Justin gave you says, and Tsjerk has since confirmed, this is >normal. There are infinitely many equivalent representations of your >simulation, not all of which will look connected for the thing that is of >interest. > >Strategies for handling visualisation are also on that link, but you don't >need to handle anything within the simulation. > >Mark > >On Thu, 14 Apr 2016 09:48 Brett <brettliu...@163.com> wrote: > >> Dear All, >> >> As I have introduced in my previous e-mail, >> >> "After energy minimization and equilibrations, I am now running a 50 ns >> production MD, for a protein of 6 identical subunits, with each subunit >> about 300 residues (from resi 120 to resi 420), and there were no breaks in >> any chain. Every day it runs about 1 ns, and every day I use the command >> trjconv to get a new PDB based on the md_0_1.trr file, for the comparison >> between the new pdb and the initial pdb. >> >> >> Today I got the PDB at 6 ns. However when I checked it my pymol, I find >> there is something very strange. Although the rmsd between the 6 ns md PDB >> and 0ns md PDB was about only 3.7, for chain B, residue 366-367 moved 180 >> angstrom away from this residues neighbouring residues, and correspondingly >> make chain B has a break at residue 366-367!" >> >> A moment ago by trjconv I regot the6 ns pdb with water, I find the residue >> 366-367 are almost (or exactly) at the edge of the water box (but by naked >> eye it seems the residue 366-367 are not outside of the water box). In this >> does the moving away of the residue 366-367 are still caused by " >> Periodic_Boundary_Conditions", and can I continue the production md to >> completion with the residue 366-367 disconnected from the major part of the >> protein complex and then I correct it by trjconv? >> >> I am looking forward to getting a reply from you. >> >> >> Brett >> >> >> >> >> >> >> >> >> >> >> Forwarding messages >> From: "Tsjerk Wassenaar" <tsje...@gmail.com> >> Date: 2016-04-14 12:16:56 >> To: "Discussion list for GROMACS users" <gmx-us...@gromacs.org> >> Subject: Re: [gmx-users] very strange phenomenon for my production MD by >> gromacs >> right! >> >> Cheers, >> >> Tsjerk >> On Apr 14, 2016 05:32, "Brett" <brettliu...@163.com> wrote: >> >> > Dear All, >> > >> > If the issue in my production MD was caused by >> > "Periodic_Boundary_Conditions", I can continue my production MD until it >> > completed, and it will not affect my final results suppose I have it >> > corrected by trjconv, right? >> > >> > >> > Brett >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > At 2016-04-13 22:37:34, "Justin Lemkul" <jalem...@vt.edu> wrote: >> > > >> > > >> > >On 4/13/16 10:30 AM, Brett wrote: >> > >> Dear All, >> > >> >> > >> >> > >> After energy minimization and equilibrations, I am now running a 50 ns >> > >> production MD, for a protein of 6 identical subunits, with each >> subunit >> > about >> > >> 300 residues (from resi 120 to resi 420), and there were no breaks in >> > any >> > >> chain. Every day it runs about 1 ns, and every day I use the command >> > trjconv >>
[gmx-users] very strange phenomenon for my production MD by gromacs
Dear All, As I have introduced in my previous e-mail, "After energy minimization and equilibrations, I am now running a 50 ns production MD, for a protein of 6 identical subunits, with each subunit about 300 residues (from resi 120 to resi 420), and there were no breaks in any chain. Every day it runs about 1 ns, and every day I use the command trjconv to get a new PDB based on the md_0_1.trr file, for the comparison between the new pdb and the initial pdb. Today I got the PDB at 6 ns. However when I checked it my pymol, I find there is something very strange. Although the rmsd between the 6 ns md PDB and 0ns md PDB was about only 3.7, for chain B, residue 366-367 moved 180 angstrom away from this residues neighbouring residues, and correspondingly make chain B has a break at residue 366-367!" A moment ago by trjconv I regot the6 ns pdb with water, I find the residue 366-367 are almost (or exactly) at the edge of the water box (but by naked eye it seems the residue 366-367 are not outside of the water box). In this does the moving away of the residue 366-367 are still caused by " Periodic_Boundary_Conditions", and can I continue the production md to completion with the residue 366-367 disconnected from the major part of the protein complex and then I correct it by trjconv? I am looking forward to getting a reply from you. Brett Forwarding messages From: "Tsjerk Wassenaar" <tsje...@gmail.com> Date: 2016-04-14 12:16:56 To: "Discussion list for GROMACS users" <gmx-us...@gromacs.org> Subject: Re: [gmx-users] very strange phenomenon for my production MD by gromacs right! Cheers, Tsjerk On Apr 14, 2016 05:32, "Brett" <brettliu...@163.com> wrote: > Dear All, > > If the issue in my production MD was caused by > "Periodic_Boundary_Conditions", I can continue my production MD until it > completed, and it will not affect my final results suppose I have it > corrected by trjconv, right? > > > Brett > > > > > > > > > > > > At 2016-04-13 22:37:34, "Justin Lemkul" <jalem...@vt.edu> wrote: > > > > > >On 4/13/16 10:30 AM, Brett wrote: > >> Dear All, > >> > >> > >> After energy minimization and equilibrations, I am now running a 50 ns > >> production MD, for a protein of 6 identical subunits, with each subunit > about > >> 300 residues (from resi 120 to resi 420), and there were no breaks in > any > >> chain. Every day it runs about 1 ns, and every day I use the command > trjconv > >> to get a new PDB based on the md_0_1.trr file, for the comparison > between the > >> new pdb and the initial pdb. > >> > >> > >> Today I got the PDB at 6 ns. However when I checked it my pymol, I find > there > >> is something very strange. Although the rmsd between the 6 ns md PDB > and 0ns > >> md PDB was about only 3.7, for chain B, residue 366-367 moved 180 > angstrom > >> away from this residues neighbouring residues, and correspondingly make > chain > >> B has a break at residue 366-367! > >> > >> > >> Will you please let me know what is wrong with my MD, and why 2 residues > >> (resi 366-367) moved 180 angstrom away? Does this phenomenon often > occur? > >> > > > > > http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > > > >-Justin > > > >-- > >== > > > >Justin A. Lemkul, Ph.D. > >Ruth L. Kirschstein NRSA Postdoctoral Fellow > > > >Department of Pharmaceutical Sciences > >School of Pharmacy > >Health Sciences Facility II, Room 629 > >University of Maryland, Baltimore > >20 Penn St. > >Baltimore, MD 21201 > > > >jalem...@outerbanks.umaryland.edu | (410) 706-7441 > >http://mackerell.umaryland.edu/~jalemkul > > > >== > >-- > >Gromacs Users mailing list > > > >* Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > >* For (un)subscribe requests visit > >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > http
Re: [gmx-users] very strange phenomenon for my production MD by gromacs
Dear All, If the issue in my production MD was caused by "Periodic_Boundary_Conditions", I can continue my production MD until it completed, and it will not affect my final results suppose I have it corrected by trjconv, right? Brett At 2016-04-13 22:37:34, "Justin Lemkul" <jalem...@vt.edu> wrote: > > >On 4/13/16 10:30 AM, Brett wrote: >> Dear All, >> >> >> After energy minimization and equilibrations, I am now running a 50 ns >> production MD, for a protein of 6 identical subunits, with each subunit about >> 300 residues (from resi 120 to resi 420), and there were no breaks in any >> chain. Every day it runs about 1 ns, and every day I use the command trjconv >> to get a new PDB based on the md_0_1.trr file, for the comparison between the >> new pdb and the initial pdb. >> >> >> Today I got the PDB at 6 ns. However when I checked it my pymol, I find there >> is something very strange. Although the rmsd between the 6 ns md PDB and 0ns >> md PDB was about only 3.7, for chain B, residue 366-367 moved 180 angstrom >> away from this residues neighbouring residues, and correspondingly make chain >> B has a break at residue 366-367! >> >> >> Will you please let me know what is wrong with my MD, and why 2 residues >> (resi 366-367) moved 180 angstrom away? Does this phenomenon often occur? >> > >http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions > >-Justin > >-- >== > >Justin A. Lemkul, Ph.D. >Ruth L. Kirschstein NRSA Postdoctoral Fellow > >Department of Pharmaceutical Sciences >School of Pharmacy >Health Sciences Facility II, Room 629 >University of Maryland, Baltimore >20 Penn St. >Baltimore, MD 21201 > >jalem...@outerbanks.umaryland.edu | (410) 706-7441 >http://mackerell.umaryland.edu/~jalemkul > >== >-- >Gromacs Users mailing list > >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] very strange phenomenon for my production MD by gromacs
Dear All, After energy minimization and equilibrations, I am now running a 50 ns production MD, for a protein of 6 identical subunits, with each subunit about 300 residues (from resi 120 to resi 420), and there were no breaks in any chain. Every day it runs about 1 ns, and every day I use the command trjconv to get a new PDB based on the md_0_1.trr file, for the comparison between the new pdb and the initial pdb. Today I got the PDB at 6 ns. However when I checked it my pymol, I find there is something very strange. Although the rmsd between the 6 ns md PDB and 0ns md PDB was about only 3.7, for chain B, residue 366-367 moved 180 angstrom away from this residues neighbouring residues, and correspondingly make chain B has a break at residue 366-367! Will you please let me know what is wrong with my MD, and why 2 residues (resi 366-367) moved 180 angstrom away? Does this phenomenon often occur? I am looking forward to getting a reply from you. Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on md of protein-ligand complex
Dear All, For a MD of a protein-ligand complex, I intend to use AMBER99SB-ILDN protein force field for the protein part. If I use the antechamber (for GAFF force field) to produce the ligand top file and gro file, can GROMCS accept this kind of antechamber produced ligand files for MD? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] questions related to MD of protein-ligand complex
Dear All, There is the on-line Justin Protein-ligand MD tutorial, but my protein complex contains 4 identical subunits and each subunit contains a ligand. In this situation should I prepare 4 ligand files using the ligand file preparation tools external to GROMCS? And what extra attention I should take for preparing the complex.gro and topol.top for this 4-ligand complex? For the "topol.top", the on-line tutorial has a sentence " Just insert a line that says #include "drg.itp" into topol.top after the position restraint file is included". Here what does it mean for the "position restraint file", and where has been included in the on-line tutorial (example files)? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] questions related to md.mdp
Dear All, Based on the on-line lysozyme tutorial, the first several lines I used for my md.mdp was as following, title= OPLS Lysozyme MD ; Run parameters integrator= md; leap-frog integrator nsteps= 500; 2 * 500 = 1 ps, 10 ns dt= 0.002; 2 fs ; Output control nstxout= 1000; save coordinates every 2 ps nstvout= 1000; save velocities every 2 ps nstenergy= 1000; save energies every 2 ps nstlog= 1000; update log file every 2 ps My first question is, besides 2 fs for the dt, can I change dt to 20 fs or 200 fs, or 2000 fs for very long production MD? And what will be the difference for the results of production MD between dt=2 fs and dt=2000 fs? My second question is, the intervals for saving coordinates, velocities, energies, log file should be same, or can the intervals different? My third question is, the intervals for saving coordinates, velocities, energies, log file should be an integer times the dt, or have no relationship with dt? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] WARNING: Incomplete frame
Dear Justin, Will you please write out the restart command for me? I am afraid without your written command I cannot do it. Brett At 2016-04-05 22:06:57, "Justin Lemkul" <jalem...@vt.edu> wrote: > > >On 4/5/16 10:04 AM, Brett wrote: >> Dear Justin, >> >> WIll you please give a reply for the following question? Most probably I >> need to restart my MD from the beginning? >> > >Restart from the last checkpoint and use -cpi -append. mdrun will overwrite >the >broken frames. No need for trjcat, trjconv, etc. > >-Justin > >> Brett >> >> >> >> >> >> >> >> At 2016-04-05 17:18:31, "Brett" <brettliu...@163.com> wrote: >> >> Dear All, >> >> >> After energy minimization and equilibration, I started a 10 ns production >> MD. By accident the production MD stopped at 450 ps (which produced >> md_0_1.trr), and I continue the production MD from the previous 450 ps point >> (which produced md_0_1_from0.45to10ns.trr). >> >> >> Then by gmx trjcat -f md_0_1.trr md_0_1_from0.45to10ns.trr -b 2330 -e 2331 >> -o md_0_12330psto2332ps.trr, I tried to get 2330-2331 frame trr file. >> However although I got the md_0_12330psto2332ps.trr, GROMAS gave a strong >> warning message: >> WARNING: Incomplete frame: nr 234 time 468 >> >> >> Will you please advise whether my " md_0_1_from0.45to10ns.trr" was totally >> broken and whether I need to restart my production MD? And why I got the >> incomplete frame? >> >> >> Brett >> >> >> >> >> >> >> >> > >-- >== > >Justin A. Lemkul, Ph.D. >Ruth L. Kirschstein NRSA Postdoctoral Fellow > >Department of Pharmaceutical Sciences >School of Pharmacy >Health Sciences Facility II, Room 629 >University of Maryland, Baltimore >20 Penn St. >Baltimore, MD 21201 > >jalem...@outerbanks.umaryland.edu | (410) 706-7441 >http://mackerell.umaryland.edu/~jalemkul > >== >-- >Gromacs Users mailing list > >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] WARNING: Incomplete frame
Dear Justin, WIll you please give a reply for the following question? Most probably I need to restart my MD from the beginning? Brett At 2016-04-05 17:18:31, "Brett" <brettliu...@163.com> wrote: Dear All, After energy minimization and equilibration, I started a 10 ns production MD. By accident the production MD stopped at 450 ps (which produced md_0_1.trr), and I continue the production MD from the previous 450 ps point (which produced md_0_1_from0.45to10ns.trr). Then by gmx trjcat -f md_0_1.trr md_0_1_from0.45to10ns.trr -b 2330 -e 2331 -o md_0_12330psto2332ps.trr, I tried to get 2330-2331 frame trr file. However although I got the md_0_12330psto2332ps.trr, GROMAS gave a strong warning message: WARNING: Incomplete frame: nr 234 time 468 Will you please advise whether my " md_0_1_from0.45to10ns.trr" was totally broken and whether I need to restart my production MD? And why I got the incomplete frame? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] several basic questions on GROMACS
Dear Justin, Suppose at the end of NVT equilibation and before the start of the following NPT equilibation, I intentionally (or by accident) delete the nvt_prev.cpt file from the directory, does it affect the run of the NPT equilibation step? Brett At 2016-04-05 21:27:41, "Justin Lemkul" <jalem...@vt.edu> wrote: > > >On 4/5/16 9:24 AM, Brett wrote: >> Dear All, >> >> Based on the on-line Lysozyme tutorial, I started a MD from energy >> minimization to NVT equlibation to NPT equlibration, and I am now in the >> production MD step. >> >> When I checked my Directory containing all the MD files for the whole MD >> process, I find there is a "mdout.mdp". Is my understanding correct on that, >> in the energy minimization step, it will create a "mdout.mdp" file, and in >> any of the following of NVT equlibation, NPT equlibration and production MD >> step, a "mdout.mdp" file will be created and automatically replaced the >> "mdout.mdp" file created in the previous step? >> > >GROMACS backs up files, it doesn't replace them unless you set >GMX_MAXBACKUP=-1. > >> As I mentioned, currently I was in the production M step, and if I >> intentionally delete the "mdout.mdp" file from the Directory, how does it >> affect my production MD? >> > >mdout.mdp is just to record your options for posterity. Deleting it has no >effect on anything. > >> The next question, during my production MD step, I checked my Directory, and >> here let me take the NVT related files as example, I found there were a >> nvt.cpt and a nvt_prev.cpt file. Suppose my NVT equilibration step lasts for >> 100 ps, is the nvt.cpt the file created by "gmx grompp -f npt.mdp -c nvt.gro >> -t nvt.cpt -p topol.top -o npt.tpr", and the nvt_prev.cpt the cpt file >> created at the end of "gmx mdrun -deffnm npt -v &", and this nvt_prev.cpt >> file will be used at the beginning of the next step NPT equilibration? >> > >Look at the time stamps. Checkpoint files are mdrun output and are written >per >the mdrun command line -cpt option, which defaults to once every 15 minutes. >A >previous checkpoint (*_prev.cpt) is written as a failsafe, in case something >goes wrong writing the current checkpoint so you don't lose all your work in >the >event of a disruption. > >-Justin > >-- >== > >Justin A. Lemkul, Ph.D. >Ruth L. Kirschstein NRSA Postdoctoral Fellow > >Department of Pharmaceutical Sciences >School of Pharmacy >Health Sciences Facility II, Room 629 >University of Maryland, Baltimore >20 Penn St. >Baltimore, MD 21201 > >jalem...@outerbanks.umaryland.edu | (410) 706-7441 >http://mackerell.umaryland.edu/~jalemkul > >== >-- >Gromacs Users mailing list > >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] several basic questions on GROMACS
Dear All, Based on the on-line Lysozyme tutorial, I started a MD from energy minimization to NVT equlibation to NPT equlibration, and I am now in the production MD step. When I checked my Directory containing all the MD files for the whole MD process, I find there is a "mdout.mdp". Is my understanding correct on that, in the energy minimization step, it will create a "mdout.mdp" file, and in any of the following of NVT equlibation, NPT equlibration and production MD step, a "mdout.mdp" file will be created and automatically replaced the "mdout.mdp" file created in the previous step? As I mentioned, currently I was in the production M step, and if I intentionally delete the "mdout.mdp" file from the Directory, how does it affect my production MD? The next question, during my production MD step, I checked my Directory, and here let me take the NVT related files as example, I found there were a nvt.cpt and a nvt_prev.cpt file. Suppose my NVT equilibration step lasts for 100 ps, is the nvt.cpt the file created by "gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr", and the nvt_prev.cpt the cpt file created at the end of "gmx mdrun -deffnm npt -v &", and this nvt_prev.cpt file will be used at the beginning of the next step NPT equilibration? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on -dt of trjcat and trjconv
Dear All, For both trjcat and trjconv, there was an option "-dt", which the on-line GROMACS material explained as following, "Only write frame when t MOD dt = first time (ps) ". Will you please explain to me what is the meaning of "Only write frame when t MOD dt = first time (ps)", by a detailed example with command? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] on non-equilibrium MD
Dear, I am still confisued, Suppose for a protein, its ligand binding form has a higher energy that its apo form. After we got the apo format PDB from the protein-ligand PDB, we energy minimized the apo protein and equlibrated it and then run production MD on it. I deduce if the final stabilized apo protein has significant different conformation from the ligand binding status, during the production MD the internal energy of the apo protein will change significantly. If the production MD cannot cross energy barrier, then how production MD can make us see significant protein conformational change during the MD? Brett At 2016-04-03 01:08:19, "Justin Lemkul" <jalem...@vt.edu> wrote: > > >On 4/1/16 10:51 PM, Brett wrote: >> Thanks Justin. >> >> Based on your answer, here I would like to ask, >> >> Suppose there is a PDB for a protein-ligand, and it is already known ligand >> would lead extremely significant conformation change of that specific >> protein. Based on the protein-ligand PDB, I would like to investigate the >> conformation of the protein without ligand by MD. >> >> First from the PDB for the protein-ligand, I delete the ligand part and get >> the PDB for the protein part. Then with the protein part PDB and based on >> your lyzoyme tutorial protocol, through energy minimization, NVT and NPT >> equilibration, I start the production MD. >> >> Here my question is, as for the energy of the protein in the ligand binding >> and ligand free state is significantly different, and based on my practice >> based on your lysozyme tutorial, the energy minimization, NVT and NPT >> equilibration steps could almost lead to no conformation change of the >> protein from the initial PDB conformation in the protein-ligand state, then > >As is their purpose. > >> in the production MD process, there should be a significant conformation >> change, which I regard that the conformation change can be checked by the >> energy change by command "gmx energy -f md_01.edr -o potential.xvg". If the > >The potential energy will be dominated by water, and the potential energy of >the >protein itself is a force field-dependent, nonphysical quantity. So no, this >doesn't give you anything useful. > >> protein conformation in the ligand binding status has much higher energy than >> in the ligand free state, then will you please tell me why the conformation >> change can only be observed in the production md process, but not in the >> initial energy minimization step before the production MD? >> > >There is no thermal energy in EM, so energy barriers are not crossed. The >structural changes are all downhill in local minima. So to observe >conformational changes in an apo protein will require extensive (and multiple) >simulations to observe, perhaps on the microsecond scale or longer. > >You can't simply skip equilibration because you know the structure will >change. > You still need to equilibrate the solvent around the initial state of the >protein; if you don't, you'll get spurious forces that (if the simulation >doesn't immediately collapse) will lead to potentially artificial structure >changes. > >-Justin > >-- >== > >Justin A. Lemkul, Ph.D. >Ruth L. Kirschstein NRSA Postdoctoral Fellow > >Department of Pharmaceutical Sciences >School of Pharmacy >Health Sciences Facility II, Room 629 >University of Maryland, Baltimore >20 Penn St. >Baltimore, MD 21201 > >jalem...@outerbanks.umaryland.edu | (410) 706-7441 >http://mackerell.umaryland.edu/~jalemkul > >== >-- >Gromacs Users mailing list > >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on crashed MD
Dear All, Before when I got a MD crashed, I do the following to continue it, "gmx tpbconv -s md_0_1.tpr -extend 0 -o md_0_1extending0ps.tpr gmx mdrun -deffnm md_0_1extending0ps -cpi md_0_1_prev.cpt -reprod -v &" Recently I have a crashed MD, and when I do "gmx tpbconv -s md_0_1.tpr -extend 0 -o md_0_1extending0ps.tpr", it says tpbconv has been replaced by convert-tpr. In "http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/onlinehelp/gmx-convert-tpr.html#gmx-convert-tpr;, there was introduction on convert-tpr, which says, "gmxconvert-tpr can edit run input files in four ways. 1. by modifying the number of steps in a run input file with options -extend, -until or -nsteps (nsteps=-1 means unlimited number of steps) 2. (OBSOLETE) by creating a run input file for a continuation run when your simulation has crashed due to e.g. a full disk, or by making a continuation run input file. This option is obsolete, since mdrun now writes and reads checkpoint files. Note that a frame with coordinates and velocities is needed. When pressure and/or Nose-Hoover temperature coupling is used an energy file can be supplied to get an exact continuation of the original run. 3. by creating a .tpx file for a subset of your original tpx file, which is useful when you want to remove the solvent from your .tpx file, or when you want to make e.g. a pure Calpha .tpx file. Note that you may need to use -nsteps-1 (or similar) to get this to work. WARNING: this .tpx file is not fully functional. 4. by setting the charges of a specified group to zero. This is useful when doing free energy estimates using the LIE (Linear Interaction Energy) method". My first question is, when I meet a crashed MD, can I continue it by "gmx convert-tpr -s md_0_1.tpr -extend 0 -o md_0_1extending0ps.tpr gmx mdrun -deffnm md_0_1extending0ps -cpi md_0_1_prev.cpt -reprod -v &"? My second question is, as for the introduction on convert-tpr says to continue a crashed MD by "gmx convert-tpr" was obsolete, will you please tell me the command by mdrun to directly continue a crashed MD? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] on non-equilibrium MD
Thanks Justin. Based on your answer, here I would like to ask, Suppose there is a PDB for a protein-ligand, and it is already known ligand would lead extremely significant conformation change of that specific protein. Based on the protein-ligand PDB, I would like to investigate the conformation of the protein without ligand by MD. First from the PDB for the protein-ligand, I delete the ligand part and get the PDB for the protein part. Then with the protein part PDB and based on your lyzoyme tutorial protocol, through energy minimization, NVT and NPT equilibration, I start the production MD. Here my question is, as for the energy of the protein in the ligand binding and ligand free state is significantly different, and based on my practice based on your lysozyme tutorial, the energy minimization, NVT and NPT equilibration steps could almost lead to no conformation change of the protein from the initial PDB conformation in the protein-ligand state, then in the production MD process, there should be a significant conformation change, which I regard that the conformation change can be checked by the energy change by command "gmx energy -f md_01.edr -o potential.xvg". If the protein conformation in the ligand binding status has much higher energy than in the ligand free state, then will you please tell me why the conformation change can only be observed in the production md process, but not in the initial energy minimization step before the production MD? Brett At 2016-04-02 10:21:33, "Justin Lemkul" <jalem...@vt.edu> wrote: > > >On 4/1/16 10:15 PM, Brett wrote: >> Dear All, >> >> For non-equilibrium MD, does it mean there would be no need for the energy >> minimization step, NVT equilibrium step and NPT equilibrium step before the >> production MD? In which situation we use non-equilibrium MD, and in which >> situation we use the production MD with energy minimization step, NVT >> equilibrium step and NPT equilibrium step? >> > >The term "non-equilibrium MD" covers a lot of different possibilities, each >with >their own applications - freezing, applying selective acceleration, pull code, >etc. There is no single answer to when these should be applied because they >are >intrinsically different. > >Just because there is some perturbing or net force on the system does not mean >you can skip all the normal preparation steps. I can practically guarantee >that >if you skip minimization and try to apply the pull code, your system will >immediately crash. Some things are always necessary, but the exact protocol >depends on the goals at hand and the specific technique(s) being applied. > >-Justin > >-- >== > >Justin A. Lemkul, Ph.D. >Ruth L. Kirschstein NRSA Postdoctoral Fellow > >Department of Pharmaceutical Sciences >School of Pharmacy >Health Sciences Facility II, Room 629 >University of Maryland, Baltimore >20 Penn St. >Baltimore, MD 21201 > >jalem...@outerbanks.umaryland.edu | (410) 706-7441 >http://mackerell.umaryland.edu/~jalemkul > >== >-- >Gromacs Users mailing list > >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on non-equilibrium MD
Dear All, For non-equilibrium MD, does it mean there would be no need for the energy minimization step, NVT equilibrium step and NPT equilibrium step before the production MD? In which situation we use non-equilibrium MD, and in which situation we use the production MD with energy minimization step, NVT equilibrium step and NPT equilibrium step? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gromacs 5.1.2 and a possible bug related to energy minimization step
Dear All, After running "gmx mdrun -v -deffnm em &", I run "gmx energy -f em.edr -o potential.xvg", but xmgrace indicated that the x-axis was "Time (ps)", although I think the value indicated by x-axis should be "step". Is it a bug? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] a question related to minim.mdp
Dear all, Following is a minim.mdp from the website, in which "nsteps = 5". Here what I want to ask is, does it mean the larger the protein, the larger the value of nsteps? Or for any size of protein regardless of mw, as for it has specified "emtol = 500.0", " nsteps = 50000" will always work? Brett minim.mdp was as following, "; ions.mdp - used as input into grompp to generate ions.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 500.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.4 ; Short-range electrostatic cut-off rvdw= 1.4 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions" -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx & terminal residues
raction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 42 named ILE of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. Before cleaning: 711 pairs Before cleaning: 847 dihedrals Making cmap torsions... There are 313 dihedrals, 181 impropers, 608 angles 711 pairs, 419 bonds and 0 virtual sites Total mass 4704.396 a.m.u. Total charge -1.000 e Writing topology Writing coordinate file... - PLEASE NOTE You have successfully generated a topology from: practice.pdb. The Gromos54a7 force field and the spc water model are used. - ETON ESAELP gcq#564: "Even if you are on the right track, you will get run over if you just sit there." (Will Rogers) -- At 2016-03-31 22:33:21, "Justin Lemkul" <jalem...@vt.edu> wrote: > > >On 3/31/16 8:18 AM, Brett wrote: >> Dear Justin and All, >> >> For terminal residue, regardless I select 0, 1, 2, the error messages always >> exist. >> >> I have opened the pdb by swiss deep view and resaved it, the same error >> message still exist. >> >> >> However if I choose force field 6: AMBER99SB-ILDN protein, the error message >> disappear. >> >> Will you please give suggestions on getting rid of the warning messages for >> the terminal residues by pdb2gmx? >> > >Please provide the full, unfiltered screen output from a functional and >nonfunctional run through pdb2gmx. There is no reason this shouldn't work out >of the box. > >-Justin > >> Brett >> >> >> >> >> >> >> >> >> >> At 2016-03-31 19:12:38, "Justin Lemkul" <jalem...@vt.edu> wrote: >>> >>> >>> On 3/30/16 10:41 PM, Brett wrote: >>>> Dear All, >>>> >>>> When I do "mx pdb2gmx -f practice.pdb -o target_processed.gro -ignh" with >>>> force >>>> field, it gave me the warning as following, >>>> >>>> "WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was >>>> mapped >>>> to an entry in the topology database, but the atom H used in >>>> an interaction of type angle in that entry is not found in the >>>> input file. Perhaps your atom and/or residue naming needs to be >>>> fixed. >>>> >>>> >>>> >>>> WARNING: WARNING: Residue 42 named ILE of a molecule in the input file was >>>> mapped >>>> to an entry in the topology database, but the atom O used in >>>> an interaction of type angle in that entry is not found in the >>>> input file. Perhaps your atom and/or residue naming needs to be >>>> fixed. >>>> " >>>> I find Residue 1 (Asp) was exactly my N-terminal residue and Residue 42 was >>>> exactly my C-terminal residue. >>>> >>>> Here I copied the coordinates part for the N- and C-terminal residues here: >>>> >>>> ATOM 17737 N ASP N 288 177.107 183.312 121.044 1.00500.00 >>>> N >>>> ATOM 17738 CA ASP N 288 177.038 182.924 122.484 1.00500.00 >>>> C >>>> ATOM 17739 CB ASP N 288 176.431 184.048 123.329 1.00500.00 >>>> C >>>> ATOM 17740 CG ASP N 288 177.329 185.261 123.401 1.00500.00 >>>> C >>>> ATOM 17741 OD1 ASP N 288 178.383 185.181 124.068 1.00500.00 >>>> O >>>> ATOM 17742 OD2 ASP N 288 176.982 186.286 122.782 1.00500.00 >>>> O >>>> ATOM 17743 C ASP N 288 176.265 181.626 122.691 1.00500.00 >>>> C >>>> ATOM 17744 O ASP N 288 176.684 180.791 123.483 1.00500.00 >>>> O >>>> ATOM 17745 N ARG N 289 175.144 181.458 121.984 1.00500.00 >>>> N >>>> (Residue 1 named ASP by GROMACS) >>>> . >>>> >>>> ATOM 18058 O SER N 328 177.424 180.662 130.523 1.00500.00 >>>> O >>>> ATOM 18059 N ILE N 329 176.478 178.748 129.872 1.00500.00 >>>> N >>>> ATOM 18060 CA ILE N 329 175.525 179.385 128.948 1.00500.00 &
Re: [gmx-users] pdb2gmx & terminal residues
Dear Justin and All, For terminal residue, regardless I select 0, 1, 2, the error messages always exist. I have opened the pdb by swiss deep view and resaved it, the same error message still exist. However if I choose force field 6: AMBER99SB-ILDN protein, the error message disappear. Will you please give suggestions on getting rid of the warning messages for the terminal residues by pdb2gmx? Brett At 2016-03-31 19:12:38, "Justin Lemkul" <jalem...@vt.edu> wrote: > > >On 3/30/16 10:41 PM, Brett wrote: >> Dear All, >> >> When I do "mx pdb2gmx -f practice.pdb -o target_processed.gro -ignh" with >> force >> field, it gave me the warning as following, >> >> "WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was >> mapped >> to an entry in the topology database, but the atom H used in >> an interaction of type angle in that entry is not found in the >> input file. Perhaps your atom and/or residue naming needs to be >> fixed. >> >> >> >> WARNING: WARNING: Residue 42 named ILE of a molecule in the input file was >> mapped >> to an entry in the topology database, but the atom O used in >> an interaction of type angle in that entry is not found in the >> input file. Perhaps your atom and/or residue naming needs to be >> fixed. >> " >> I find Residue 1 (Asp) was exactly my N-terminal residue and Residue 42 was >> exactly my C-terminal residue. >> >> Here I copied the coordinates part for the N- and C-terminal residues here: >> >> ATOM 17737 N ASP N 288 177.107 183.312 121.044 1.00500.00 >> N >> ATOM 17738 CA ASP N 288 177.038 182.924 122.484 1.00500.00 >> C >> ATOM 17739 CB ASP N 288 176.431 184.048 123.329 1.00500.00 >> C >> ATOM 17740 CG ASP N 288 177.329 185.261 123.401 1.00500.00 >> C >> ATOM 17741 OD1 ASP N 288 178.383 185.181 124.068 1.00500.00 >> O >> ATOM 17742 OD2 ASP N 288 176.982 186.286 122.782 1.00500.00 >> O >> ATOM 17743 C ASP N 288 176.265 181.626 122.691 1.00500.00 >> C >> ATOM 17744 O ASP N 288 176.684 180.791 123.483 1.00500.00 >> O >> ATOM 17745 N ARG N 289 175.144 181.458 121.984 1.00500.00 >> N >> (Residue 1 named ASP by GROMACS) >> . >> >> ATOM 18058 O SER N 328 177.424 180.662 130.523 1.00500.00 >> O >> ATOM 18059 N ILE N 329 176.478 178.748 129.872 1.00500.00 >> N >> ATOM 18060 CA ILE N 329 175.525 179.385 128.948 1.00500.00 >> C >> ATOM 18061 CB ILE N 329 174.867 178.368 127.980 1.00499.43 >> C >> ATOM 18062 CG1 ILE N 329 175.920 177.731 127.065 1.00498.96 >> C >> ATOM 18063 CD1 ILE N 329 175.462 176.450 126.400 1.00498.79 >> C >> ATOM 18064 CG2 ILE N 329 173.789 179.040 127.126 1.00498.79 >> C >> ATOM 18065 C ILE N 329 174.437 180.100 129.753 1.00498.62 >> C >> ATOM 18066 O ILE N 329 173.671 179.471 130.483 1.00498.27 >> O >> ATOM 18067 O ILE N 329 174.302 181.322 129.689 1.00496.91 >> O >> (Residue 42 named ILE by GROMACS) >> TER >> END >> >> I myself cannot find anything wrong for my 2 terminal residues. >> >> Will you please take a look to see how to modify the 2 terminal residues so >> that >> the pdb2gmx will not give the warning messages? >> >> I am looking forward to getting a reply from you. >> > >The only way the above errors would show up is if you chose "None" for your >termini; choosing an appropriate NH3+/COO- will correct this. Note you have >two >"O" in your C-terminal ILE, which is wrong as there should only be one, the >other should be OXT or whatever the force field wants (but again, the .tdb >patching mechanism takes care of this). > >-Justin > >-- >== > >Justin A. Lemkul, Ph.D. >Ruth L. Kirschstein NRSA Postdoctoral Fellow > >Department of Pharmaceutical Sciences >School of Pharmacy >Health Sciences Facility II, Room 629 >University of Maryland, Baltimore >20 Penn St. >Baltimore, MD 21201 > >jalem...@outerbanks.umaryland.edu | (410) 706-7441 >http://mackerell.umaryland.edu/~jalemkul > >== >-- >Gromacs Users mailing list > >* Please s
[gmx-users] pdb2gmx & terminal residues
Dear All, When I do "mx pdb2gmx -f practice.pdb -o target_processed.gro -ignh" with force field, it gave me the warning as following, "WARNING: WARNING: Residue 1 named ASP of a molecule in the input file was mapped to an entry in the topology database, but the atom H used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. WARNING: WARNING: Residue 42 named ILE of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. " I find Residue 1 (Asp) was exactly my N-terminal residue and Residue 42 was exactly my C-terminal residue. Here I copied the coordinates part for the N- and C-terminal residues here: ATOM 17737 N ASP N 288 177.107 183.312 121.044 1.00500.00 N ATOM 17738 CA ASP N 288 177.038 182.924 122.484 1.00500.00 C ATOM 17739 CB ASP N 288 176.431 184.048 123.329 1.00500.00 C ATOM 17740 CG ASP N 288 177.329 185.261 123.401 1.00500.00 C ATOM 17741 OD1 ASP N 288 178.383 185.181 124.068 1.00500.00 O ATOM 17742 OD2 ASP N 288 176.982 186.286 122.782 1.00500.00 O ATOM 17743 C ASP N 288 176.265 181.626 122.691 1.00500.00 C ATOM 17744 O ASP N 288 176.684 180.791 123.483 1.00500.00 O ATOM 17745 N ARG N 289 175.144 181.458 121.984 1.00500.00 N (Residue 1 named ASP by GROMACS) . ATOM 18058 O SER N 328 177.424 180.662 130.523 1.00500.00 O ATOM 18059 N ILE N 329 176.478 178.748 129.872 1.00500.00 N ATOM 18060 CA ILE N 329 175.525 179.385 128.948 1.00500.00 C ATOM 18061 CB ILE N 329 174.867 178.368 127.980 1.00499.43 C ATOM 18062 CG1 ILE N 329 175.920 177.731 127.065 1.00498.96 C ATOM 18063 CD1 ILE N 329 175.462 176.450 126.400 1.00498.79 C ATOM 18064 CG2 ILE N 329 173.789 179.040 127.126 1.00498.79 C ATOM 18065 C ILE N 329 174.437 180.100 129.753 1.00498.62 C ATOM 18066 O ILE N 329 173.671 179.471 130.483 1.00498.27 O ATOM 18067 O ILE N 329 174.302 181.322 129.689 1.00496.91 O (Residue 42 named ILE by GROMACS) TER END I myself cannot find anything wrong for my 2 terminal residues. Will you please take a look to see how to modify the 2 terminal residues so that the pdb2gmx will not give the warning messages? I am looking forward to getting a reply from you. Brett At 2016-03-31 07:13:55, "Justin Lemkul" <jalem...@vt.edu> wrote: > > >On 3/30/16 8:16 AM, Brett wrote: >> Dear All, >> >> When I work with pdb2gmx for force field 54a7, I meet the following >> >> "WARNING: Residue 54 named ILE of a molecule in the input file was mapped >> to an entry in the topology database, but the atom O used in >> an interaction of type angle in that entry is not found in the >> input file. Perhaps your atom and/or residue naming needs to be >> fixed". >> >> Why you please let me know how to localize the topology database and how to >> localize ILE in the topology database , so that I can compare the atom O >> with that in my input pdb file, for fix of my pdb file? >> > >The error is explicit - you are missing an O atom (backbone carbonyl oxygen) >in >your coordinates. You need to fix any missing atoms or residues. > >-Justin > >-- >== > >Justin A. Lemkul, Ph.D. >Ruth L. Kirschstein NRSA Postdoctoral Fellow > >Department of Pharmaceutical Sciences >School of Pharmacy >Health Sciences Facility II, Room 629 >University of Maryland, Baltimore >20 Penn St. >Baltimore, MD 21201 > >jalem...@outerbanks.umaryland.edu | (410) 706-7441 >http://mackerell.umaryland.edu/~jalemkul > >== >-- >Gromacs Users mailing list > >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] a fatal error in step mdrun -v -deffnm em
gmx genion -s ions.tpr -o target_solv_ions.gro -p topol.top -pname NA -nname CL -neutral -conc 0.15 At 2016-03-30 21:38:49, "SAKO MIRZAIE" <sako.bioc...@gmail.com> wrote: >let me see your neutralizing command to produce ions.tpr. > >On 3/30/16, Brett <brettliu...@163.com> wrote: >> Dear All, >> >> After steps for pdb2gmx, editconf, solvate, "-f ions.mdp -c target_solv.gro >> -p topol.top -o ions.tpr", genion, "grompp -f minim.mdp -c >> target_solv_ions.gro -p topol.top -o em.tpr", I started step "mdrun -v >> -deffnm em &", but in the "mdrun -v -deffnm em &" step it gave >> >> "Step= 15, Dmax= 1.3e-01 nm, Epot= -4.22195e+07 Fmax= 7.18492e+04, atom= >> 7837 >> Step= 16, Dmax= 1.5e-01 nm, Epot= -4.23771e+07 Fmax= 1.46229e+05, atom= >> 5656 >> Step= 17, Dmax= 1.8e-01 nm, Epot= -4.24412e+07 Fmax= 7.58589e+05, atom= >> 5656 >> >> Back Off! I just backed up step18b_n8.pdb to ./#step18b_n8.pdb.1# >> >> Back Off! I just backed up step18c_n8.pdb to ./#step18c_n8.pdb.1# >> Wrote pdb files with previous and current coordinates >> >> --- >> Program gmx mdrun, VERSION 5.1.2 >> Source code file: >> /home/FANFENGHUI/Desktop/WORK2016_2/GROMACS/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, >> line: 555 >> >> Fatal error: >> >> step 18: Water molecule starting at atom 964420 can not be settled. >> Check for bad contacts and/or reduce the timestep if appropriate. >> " >> >> My minim.mdp was as following, >> >> "; ions.mdp - used as input into grompp to generate ions.tpr >> ; Parameters describing what to do, when to stop and what to save >> integrator = steep ; Algorithm (steep = steepest descent minimization) >> emtol = 500.0; Stop minimization when the maximum force < 1000.0 >> kJ/mol/nm >> emstep = 0.01 ; Energy step size >> nsteps = 5 ; Maximum number of (minimization) steps to perform >> >> ; Parameters describing how to find the neighbors of each atom and how to >> calculate the interactions >> nstlist = 1 ; Frequency to update the neighbor list and long >> range forces >> cutoff-scheme = Verlet >> ns_type = grid ; Method to determine neighbor list (simple, grid) >> coulombtype = PME ; Treatment of long range electrostatic >> interactions >> rcoulomb= 1.4 ; Short-range electrostatic cut-off >> rvdw= 1.4 ; Short-range Van der Waals cut-off >> pbc = xyz ; Periodic Boundary Conditions" >> >> Will you please let me know why the fatal error in step 18 occurred, and how >> to avid it? >> >> Based on "Step= 16, Dmax= 1.5e-01 nm, Epot= -4.23771e+07 Fmax= >> 1.46229e+05, atom= 5656", does it mean that step only works on atop "5656"? >> If so, if my system contains 500,000 atoms, how much should be the >> appropriate value for "nsteps" in the minim.mdp file? >> >> Brett >> >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >> mail to gmx-users-requ...@gromacs.org. >> > > >-- >*** >sako mirzaie >PhD in biochemistry, science faculty, Islamic azad university of >sanandaj, sanandaj, Iran >http://www.iausdj.ac.ir/fa/fa-info.aspx?p=s.mirzaie > >http://www.iausdj.ac.ir/en/en.aspx?p=s.mirzaie > >http://scholar.google.com/citations?user=viwZvVAJ=en > >http://www.scopus.com/authid/detail.url?authorId=54886431500 > >http://www.ncbi.nlm.nih.gov/pubmed/?term=sako+mirzaie >https://www.researchgate.net/profile/Sako_Mirzaie/publications/ >-- >Gromacs Users mailing list > >* Please search the archive at >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > >* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >* For (un)subscribe requests visit >https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] a fatal error in step mdrun -v -deffnm em
Dear All, After steps for pdb2gmx, editconf, solvate, "-f ions.mdp -c target_solv.gro -p topol.top -o ions.tpr", genion, "grompp -f minim.mdp -c target_solv_ions.gro -p topol.top -o em.tpr", I started step "mdrun -v -deffnm em &", but in the "mdrun -v -deffnm em &" step it gave "Step= 15, Dmax= 1.3e-01 nm, Epot= -4.22195e+07 Fmax= 7.18492e+04, atom= 7837 Step= 16, Dmax= 1.5e-01 nm, Epot= -4.23771e+07 Fmax= 1.46229e+05, atom= 5656 Step= 17, Dmax= 1.8e-01 nm, Epot= -4.24412e+07 Fmax= 7.58589e+05, atom= 5656 Back Off! I just backed up step18b_n8.pdb to ./#step18b_n8.pdb.1# Back Off! I just backed up step18c_n8.pdb to ./#step18c_n8.pdb.1# Wrote pdb files with previous and current coordinates --- Program gmx mdrun, VERSION 5.1.2 Source code file: /home/FANFENGHUI/Desktop/WORK2016_2/GROMACS/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line: 555 Fatal error: step 18: Water molecule starting at atom 964420 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. " My minim.mdp was as following, "; ions.mdp - used as input into grompp to generate ions.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 500.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.4 ; Short-range electrostatic cut-off rvdw= 1.4 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions" Will you please let me know why the fatal error in step 18 occurred, and how to avid it? Based on "Step= 16, Dmax= 1.5e-01 nm, Epot= -4.23771e+07 Fmax= 1.46229e+05, atom= 5656", does it mean that step only works on atop "5656"? If so, if my system contains 500,000 atoms, how much should be the appropriate value for "nsteps" in the minim.mdp file? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] a fatal error in step mdrun -v -deffnm em
Dear All, After steps for pdb2gmx, editconf, solvate, "-f ions.mdp -c target_solv.gro -p topol.top -o ions.tpr", genion, "grompp -f minim.mdp -c target_solv_ions.gro -p topol.top -o em.tpr", I started step "mdrun -v -deffnm em &", but in the "mdrun -v -deffnm em &" step it gave "Step= 15, Dmax= 1.3e-01 nm, Epot= -4.22195e+07 Fmax= 7.18492e+04, atom= 7837 Step= 16, Dmax= 1.5e-01 nm, Epot= -4.23771e+07 Fmax= 1.46229e+05, atom= 5656 Step= 17, Dmax= 1.8e-01 nm, Epot= -4.24412e+07 Fmax= 7.58589e+05, atom= 5656 Back Off! I just backed up step18b_n8.pdb to ./#step18b_n8.pdb.1# Back Off! I just backed up step18c_n8.pdb to ./#step18c_n8.pdb.1# Wrote pdb files with previous and current coordinates --- Program gmx mdrun, VERSION 5.1.2 Source code file: /home/FANFENGHUI/Desktop/WORK2016_2/GROMACS/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line: 555 Fatal error: step 18: Water molecule starting at atom 964420 can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. " My minim.mdp was as following, "; ions.mdp - used as input into grompp to generate ions.tpr ; Parameters describing what to do, when to stop and what to save integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 500.0; Stop minimization when the maximum force < 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces cutoff-scheme = Verlet ns_type = grid ; Method to determine neighbor list (simple, grid) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb= 1.4 ; Short-range electrostatic cut-off rvdw= 1.4 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions" Will you please let me know why the fatal error in step 18 occurred, and how to avid it? Based on "Step= 16, Dmax= 1.5e-01 nm, Epot= -4.23771e+07 Fmax= 1.46229e+05, atom= 5656", does it mean that step only works on atop "5656"? If so, if my system contains 500,000 atoms, how much should be the appropriate value for "nsteps" in the minim.mdp file? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] 54a7 force field & pdb2gmx & topology database
Dear All, When I work with pdb2gmx for force field 54a7, I meet the following "WARNING: Residue 54 named ILE of a molecule in the input file was mapped to an entry in the topology database, but the atom O used in an interaction of type angle in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed". Why you please let me know how to localize the topology database and how to localize ILE in the topology database , so that I can compare the atom O with that in my input pdb file, for fix of my pdb file? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on the gromacs force field for keep helix
Dear All, Before I read some on-line material , perhaps the on-line tutorial of Justin. It said there was a gromacs force field better than the other gromacs force field for keeping the intact of the helix during MD. WIll you please tell me which is the force field used for keeping the intact of the helix? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] gromacs-5.1 installation error
Dear All, When I tried to install the gromacs-5.1 by "tar xfz gromacs-5.1.tar.gz cd gromacs-5.1 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON make make check sudo make install source /usr/local/gromacs/bin/GMXRC". at the "cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON" step I met the following errors thus the gromacs-5.1 cannot be installed. Will you please explain to me on how to have the issue settled so that I can have the gromacs-5.1 installed? I am looking forward to getting a reply from you. Best regards. Brett Apache/2.2.22 (Ubuntu) Server at gerrit.gromacs.org Port 80 Connection #0 to host gerrit.gromacs.org left intact Issue another request to this URL: 'https://kth.box.com/shared/static/348ua1yqu0rh8r2gpcf6m4zvpikaarxw.gz' libcurl was built with SSL disabled, https: not supported! unsupported protocol Closing connection #0 -- Configuring incomplete, errors occurred! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on CHARMM-GUI produced lipid bilayer for gromacs use
Dear All, After I got the membrane protein PDB with the membrane part packed in lipid bilayer by the lipid bilayer builder of CHARMM-GUI, will you please let me know how to get the inputs for the gromacs next step MD process？ For example， if I wand to go directly to the nvt equilibration step with the CHARMM-GUI produced PDB, the command in the lysozyme tutorial is "gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr". Then will you please let me know how to get the input *.gro and *.top file in order to get the *.tpr file? Or for the CHARMM-GUI produced PDB, I delete all the H2O, and then start from the pdb2gmx step with the PDB file containing only the membrane protein and the lipid bilayer? But in this way it seems the sides of the lipid bilayer will also be packed in H2O. I am looking forward to getting a reply from you. Best regards. Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] membrane protein simulation
Thanks for the reply Tsjerk. In fact I am just wonding if the situation exist, i.e., for the 10th trans-membrane helices in the protein, the 8th and or 9th for example is/are a little shorter than the other several helices. Will you please give a comment on how to process this kind of membrane protein embeding in lipid Tsjerk? Brett At 2015-09-13 15:19:56, "Tsjerk Wassenaar" <tsje...@gmail.com> wrote: >Hi Brett, > >Say I'm designing this new type of truck. Because the earth it's riding >over is round, do you think I need to adjust the wheel positions on front >and back to match the curvature of the earth? > >Cheers, > >Tsjerk >On Sep 13, 2015 08:52, "Brett" <brettliu...@163.com> wrote: > >> >> Dear All, >> >> Suppose a membrane protein contains 10 trans-membrane helix, and as the >> cell membrane is round, the upper and lower part of the 10 trans- membrane >> are not horizontal as they are part of the rounded cell, will you please >> introduce to me how to make the lipid bilayer in curve to parallel the >> upper and lower part of the 10 tran- membrane? I only know we can pack the >> membrane protein into the lipid bilayer in the way the lipid bilayer would >> be perpendicular to the membrane protein. >> >> Yesterday I have posted a similar question but my post was not show in the >> post list. >> >> I am looking forward to getting your reply. >> >> >> Best regards. >> >> >> Brett >> >> >> >> >> >> >> >> >> Forwarding messages >> From: "Machtens, Jan-Philipp" <j.macht...@fz-juelich.de> >> Date: 2015-09-10 16:41:33 >> To: "gromacs.org_gmx-users@maillist.sys.kth.se" < >> gromacs.org_gmx-users@maillist.sys.kth.se> >> Subject: Re: [gmx-users] Multiple membrane proteins in complex bilayer >> (martini) >> Hi Kathrin, >> if I remember correctly I once did something similar with g_membed -pieces >> ! >> >> Cheers, >> >> Dr. Jan-Philipp Machtens >> Institute of Complex Systems - Zelluläre Biophysik (ICS-4) >> Forschungszentrum Jülich, Germany >> Telefon: 02461 616467 >> >> >> >> Date: Thu, 10 Sep 2015 01:25:00 +0200 >> From: Kathrin Hadasch <kh...@web.de> >> To: gromacs.org_gmx-users@maillist.sys.kth.se >> Subject: [gmx-users] Multiple membrane proteins in complex bilayer >> (martini) >> Message-ID: <55f0bfcc.7060...@web.de> >> Content-Type: text/plain; charset=ISO-8859-15; format=flowed >> >> Hey you all, >> I'm searching for a way to insert and embed multiple(!) copies of the >> same protein in a complex, presimulated membrane patch (all martini-cg). >> I've tryed lambada for insertion, but I couldn't get it to work with >> more than one protein. I've tried to translate the protein to a (4 4 0) >> vector with editconf in the lambada script, but I get following error: >> Modification of non-creatable array value attempted, subscript -6 at >> /home/lambada/modules/protein.pm line 281. >> For insertion via vmd, I have no clue how to generate a psf file for >> martini-lipids. >> Any suggestions how I could make it work? >> Best regards and thanks in advance, >> Kathrin >> >> >> >> >> >> >> Forschungszentrum Juelich GmbH >> 52425 Juelich >> Sitz der Gesellschaft: Juelich >> Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 >> Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher >> Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), >> Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, >> Prof. Dr. Sebastian M. Schmidt >> >> >> >> >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kt
[gmx-users] membrane protein simulation
Dear All, Suppose a membrane protein contains 10 trans-membrane helix, and as the cell membrane is round, the upper and lower part of the 10 trans- membrane are not horizontal as they are part of the rounded cell, will you please introduce to me how to make the lipid bilayer in curve to parallel the upper and lower part of the 10 tran- membrane? I only know we can pack the membrane protein into the lipid bilayer in the way the lipid bilayer would be perpendicular to the membrane protein. Yesterday I have posted a similar question but my post was not show in the post list. I am looking forward to getting your reply. Best regards. Brett Forwarding messages From: "Machtens, Jan-Philipp" <j.macht...@fz-juelich.de> Date: 2015-09-10 16:41:33 To: "gromacs.org_gmx-users@maillist.sys.kth.se" <gromacs.org_gmx-users@maillist.sys.kth.se> Subject: Re: [gmx-users] Multiple membrane proteins in complex bilayer (martini) Hi Kathrin, if I remember correctly I once did something similar with g_membed -pieces ! Cheers, Dr. Jan-Philipp Machtens Institute of Complex Systems - Zelluläre Biophysik (ICS-4) Forschungszentrum Jülich, Germany Telefon: 02461 616467 Date: Thu, 10 Sep 2015 01:25:00 +0200 From: Kathrin Hadasch <kh...@web.de> To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Multiple membrane proteins in complex bilayer (martini) Message-ID: <55f0bfcc.7060...@web.de> Content-Type: text/plain; charset=ISO-8859-15; format=flowed Hey you all, I'm searching for a way to insert and embed multiple(!) copies of the same protein in a complex, presimulated membrane patch (all martini-cg). I've tryed lambada for insertion, but I couldn't get it to work with more than one protein. I've tried to translate the protein to a (4 4 0) vector with editconf in the lambada script, but I get following error: Modification of non-creatable array value attempted, subscript -6 at /home/lambada/modules/protein.pm line 281. For insertion via vmd, I have no clue how to generate a psf file for martini-lipids. Any suggestions how I could make it work? Best regards and thanks in advance, Kathrin Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] membrane protein simulation
Dear Tsjerk, Thanks for the reply. Will you please introduce to me sevral membrane builders whith results compatible with gromacs, especially on-line available membrane builders? Best regards. Brett At 2015-09-13 17:45:52, "Tsjerk Wassenaar" <tsje...@gmail.com> wrote: >Hi Brett, > >So apart from the curvature of the membrane, there maybe the situation that >there's just more of the protein in one leaflet than in the other. You'll >need to account for that when embedding. Membrane builders typically check >for overlaps to take care of this. > >Cheers, > >Tsjerk >On Sep 13, 2015 11:37, "Brett" <brettliu...@163.com> wrote: > >> Thanks for the reply Tsjerk. In fact I am just wonding if the situation >> exist, i.e., for the 10th trans-membrane helices in the protein, the 8th >> and or 9th for example is/are a little shorter than the other several >> helices. Will you please give a comment on how to process this kind of >> membrane protein embeding in lipid Tsjerk? >> >> Brett >> >> >> >> >> >> >> >> At 2015-09-13 15:19:56, "Tsjerk Wassenaar" <tsje...@gmail.com> wrote: >> >Hi Brett, >> > >> >Say I'm designing this new type of truck. Because the earth it's riding >> >over is round, do you think I need to adjust the wheel positions on front >> >and back to match the curvature of the earth? >> > >> >Cheers, >> > >> >Tsjerk >> >On Sep 13, 2015 08:52, "Brett" <brettliu...@163.com> wrote: >> > >> >> >> >> Dear All, >> >> >> >> Suppose a membrane protein contains 10 trans-membrane helix, and as the >> >> cell membrane is round, the upper and lower part of the 10 trans- >> membrane >> >> are not horizontal as they are part of the rounded cell, will you please >> >> introduce to me how to make the lipid bilayer in curve to parallel the >> >> upper and lower part of the 10 tran- membrane? I only know we can pack >> the >> >> membrane protein into the lipid bilayer in the way the lipid bilayer >> would >> >> be perpendicular to the membrane protein. >> >> >> >> Yesterday I have posted a similar question but my post was not show in >> the >> >> post list. >> >> >> >> I am looking forward to getting your reply. >> >> >> >> >> >> Best regards. >> >> >> >> >> >> Brett >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Forwarding messages >> >> From: "Machtens, Jan-Philipp" <j.macht...@fz-juelich.de> >> >> Date: 2015-09-10 16:41:33 >> >> To: "gromacs.org_gmx-users@maillist.sys.kth.se" < >> >> gromacs.org_gmx-users@maillist.sys.kth.se> >> >> Subject: Re: [gmx-users] Multiple membrane proteins in complex bilayer >> >> (martini) >> >> Hi Kathrin, >> >> if I remember correctly I once did something similar with g_membed >> -pieces >> >> ! >> >> >> >> Cheers, >> >> >> >> Dr. Jan-Philipp Machtens >> >> Institute of Complex Systems - Zelluläre Biophysik (ICS-4) >> >> Forschungszentrum Jülich, Germany >> >> Telefon: 02461 616467 >> >> >> >> >> >> >> >> Date: Thu, 10 Sep 2015 01:25:00 +0200 >> >> From: Kathrin Hadasch <kh...@web.de> >> >> To: gromacs.org_gmx-users@maillist.sys.kth.se >> >> Subject: [gmx-users] Multiple membrane proteins in complex bilayer >> >> (martini) >> >> Message-ID: <55f0bfcc.7060...@web.de> >> >> Content-Type: text/plain; charset=ISO-8859-15; format=flowed >> >> >> >> Hey you all, >> >> I'm searching for a way to insert and embed multiple(!) copies of the >> >> same protein in a complex, presimulated membrane patch (all martini-cg). >> >> I've tryed lambada for insertion, but I couldn't get it to work with >> >> more than one protein. I've
[gmx-users] Question: Fw:Re: Multiple membrane proteins in complex bilayer (martini)
Dear All, Suppose a membrane protein contains 10 trans-membrane helix, and thus the upper and lower part of the 10 trans- membrane are not horizontal, will you please introduce to me how to make the lipid bilayer in curve to parallel the upper and lower part of the 10 tran- membrane? Best regards. Brett Forwarding messages From: "Machtens, Jan-Philipp" <j.macht...@fz-juelich.de> Date: 2015-09-10 16:41:33 To: "gromacs.org_gmx-users@maillist.sys.kth.se" <gromacs.org_gmx-users@maillist.sys.kth.se> Subject: Re: [gmx-users] Multiple membrane proteins in complex bilayer (martini) Hi Kathrin, if I remember correctly I once did something similar with g_membed -pieces ! Cheers, Dr. Jan-Philipp Machtens Institute of Complex Systems - Zelluläre Biophysik (ICS-4) Forschungszentrum Jülich, Germany Telefon: 02461 616467 Date: Thu, 10 Sep 2015 01:25:00 +0200 From: Kathrin Hadasch <kh...@web.de> To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Multiple membrane proteins in complex bilayer (martini) Message-ID: <55f0bfcc.7060...@web.de> Content-Type: text/plain; charset=ISO-8859-15; format=flowed Hey you all, I'm searching for a way to insert and embed multiple(!) copies of the same protein in a complex, presimulated membrane patch (all martini-cg). I've tryed lambada for insertion, but I couldn't get it to work with more than one protein. I've tried to translate the protein to a (4 4 0) vector with editconf in the lambada script, but I get following error: Modification of non-creatable array value attempted, subscript -6 at /home/lambada/modules/protein.pm line 281. For insertion via vmd, I have no clue how to generate a psf file for martini-lipids. Any suggestions how I could make it work? Best regards and thanks in advance, Kathrin Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Lambada + InflateGRO2 and membrane protein simulation
Dear All, Is any on-line server related to Lambada + InflateGRO2, which can gives the PDB file of the target membrane protein for simulation, including the coordinates of the surrounding lipid bilaylayer molecules? I am looking forward to getting a reply from you. Best regards. Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on MD simulation of ATP hydrolysis driven protein conformational change
Dear All, There are some biological processes involving ATP hydrolysis driven protein conformational change. By MD, can we simulate the protein global conformational change driven by ATP hydrolysis? Or by MD can we investigate how the energy stored in ATP converts to protein conformational change? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on VMD analysis of the gromacs production MD
Dear All, After energy minimization, 100 ps NVT md and 100 ps NPT md (based on the on-line lysozyme tutorial), I have processed a 30 ns production MD (also based on the on-line lysozyme tutorial). Then I load the NPT.gro and the 30ns_production_md.xtc to the VMD, and by VMD I find in the whole 30 ns md, the whole protein molecule has an about 50 degree rotation (the 50 degree occurs gradually in the 15 ns md, not a sudden 50 degree rotation). Is this 50 degree rotation normal or abnormal? If by VMD I want to observe the local conformation changes in the whole 30 ns md, rather than the global 50 degree rotation, will you please tell me which trajectory file I need to load to VMD, and by which command I can get that trajectory file? Best regards. Smith -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on trjconv command
Dear All, Will you please show me the command based on the following cited content from the website on how to convert a xtc file with 1 frame per 2 ps to a xtc file with 1 frame per 10 ps? I hope the command contains “-dt” and “-timestep”， and what the values should be for “-dt” and “-timestep”. Best regards Brett With -dt it is possible to reduce the number of frames in the output. This option relies on the accuracy of the times in your input trajectory, so if these are inaccurate use the -timestep option to modify the time (this can be done simultaneously). -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on trjcat command
Dear All, The command trjcat can be used for connection of trr files and xtc files in the similar manner, and suppose the first MD is from 0 to 1 ns, the second MD is from 1 ns to 4 ns, the third MD is from 4 ns to 4.5 ns, by trjcat we can get the whole trr file from 0 nx to 4.5 ns, and if the input is the xtc files, we can then get the whole xtc file from 0 nx to 4.5 ns, am I right? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on the gmx solvate command
Dear All, Before I neutralize my system with the genion command, I solvate it with the gmx solvate command, it writes, System total charge: 0.00. But the pdb2gmx step clearly indicate the systemp has -62 negative charges. Will you please explain to me why the gmx solvate step can show the system as without charge? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on g_covar to produce average structure
Dear All, The on-line tutorial says, Warning – Average structures (by g_covar) tend to be crude. Minimization is recommended. Here the minmization should be the energy minization step before the NVT and NPT equilibration steps, for our preparation of the files for the production md, right? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on a MD run notice
Dear All, For a NVT equilibration MD, I got the following notice. Will you please advice me whether the notice just told me I have wasted my computation resource, or I need to redo my NVT equilibration. I am looking forward to getting your reply. Brett verage load imbalance: 7.7 % Part of the total run time spent waiting due to load imbalance: 3.8 % Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 0 % Y 0 % Average PME mesh/force load: 0.228 Part of the total run time spent waiting due to PP/PME imbalance: 9.3 % NOTE: 9.3 % performance was lost because the PME ranks had less work to do than the PP ranks. You might want to decrease the number of PME ranks or decrease the cut-off and the grid spacing. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] MPI command For MD
Dear All， Will you please paste the commands for MD (including file preparation ) if the computer contains more than 10 cores? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] the relationship between mdp file and the force field
Dear Justin, I have read some of the force fields original paper, but my purpose is to use MD to settle some biological issues, thus I am afraid I do not have such deep understanding what explained in the original force field papers. For Force field 6, here I mean AMBER99SB_ILDNprotein. For the MDP files, I think AMBER99SB_ILDNprotein force field, AMBER99SB protein, AMBER 99 protein, AMBER 96 protein can have the same mdp files, GROMOS96 43a1, 43a2, 45a3, 53a3, 53a5,53a6,54a7 can have the same MDP files, am I right? If we modified based on the on-line lysozyme tutorial, what items should we modify based on the original lysozyme mdp diles? In addition, for biological research, can we definetely say GROMOS96 54a7 is better than the other versions of GROMOS96? In comparision with the GROMOS series, what is the advantages and disavantages of OPLS-AA/L all-atom force field? I am looking forward to getting a reply from you. Best regards. Brett At 2015-04-27 19:41:17, Justin Lemkul jalem...@vt.edu wrote: On 4/26/15 10:17 PM, Brett wrote: Dear All, In the on-line Justin tutorial on lysozyme, the several mdp files are for the specific force field OPLS-AA force field. It specifically mentioned Settings, particularly nonbonded interaction settings, will be different for other force fields. Will you please introduce to me how to modify mdp files based on the difference of the force fields? For example, if I use force field 6, what should I modify based on the mdps of the lysozyme tutorial? I am looking forward to getting your reply. Force field 6 is not very precise, because the numbering in the pdb2gmx list varies between GROMACS versions. What force field (exactly) are you using? Have you read the primary literature for the force field? Settings are given in the parametrization/validation papers and that's what you should use. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on rlist
Dear All, In the MD mdp file for the old version of on-line tutorials for lysozyme, in the neighbor search, there is an item rlist, but in the MD mdp file for the new version of on-line tutorials for lysozyme, in the neighbor search, there is no item rlist. Will you please tell me why? In addition, as Verlet has been selected, what is the meaning of nstlist = 10; 20 fs, largely irrelevant with Verlet ? I am looking forward to getting your reply. Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on the MDP options
Dear All, In the on-line lysozyme tutorial, it gives a series of mdp files. But it meantioned for different force fields the options should be different. Will you please tell me regardless of force fields, whether all the cutoff-scheme can be Verlet? Besides I can change the rcoulomb and rvdw fom 1.0 to 1.4, what else should I change on the basis of the on-line tutorial MDP files, with the difference of the force fields? I am looking forward to getting your reply. Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on the xmgrac for gromacs
Dear All, For the grpmacs analysis purpose, from the official GRACE site I have downloaded and installed different versions of GRACE, some was said to definitely contains xmgrace. But after installation, none contains xmgrace, they contain grace or gr in the bin folder. After I invoke the grace or gr, both needs me input commands, and if I input grace -nxy potential.xvg, they did not work. My workstation is a red hat linux system, and I do not know whether there is X windows installed. Will you please let me know how to have my xmgrace -nxy potential.xvg function works? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] on the xmgrac for gromacs
The issue is, no mater grace or xmggrace I download, I cannot have the xmgrace exe file in the corresponding bin folder produced. Thus will you tell me which version of grace has the xmgrace after unpack and installation? Brett At 2015-04-26 23:09:23, abhijit Kayal abhijitchemi...@gmail.com wrote: the command is xmgrace, try with xmgrace -nxy. On Sun, Apr 26, 2015 at 7:01 AM, Brett brettliu...@163.com wrote: Dear All, For the grpmacs analysis purpose, from the official GRACE site I have downloaded and installed different versions of GRACE, some was said to definitely contains xmgrace. But after installation, none contains xmgrace, they contain grace or gr in the bin folder. After I invoke the grace or gr, both needs me input commands, and if I input grace -nxy potential.xvg, they did not work. My workstation is a red hat linux system, and I do not know whether there is X windows installed. Will you please let me know how to have my xmgrace -nxy potential.xvg function works? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Abhijit kayal Research Scholar Theoretical Chemistry IIT Kanpur -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] a question related to gmx energy minimization
Dear Tsjerk, Will you please explain to me why the RMSD in this step is so large? For this reason I think there is something wrong. I am looking forward to getting a reply from you. Brett At 2015-04-26 20:59:59, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Brett, Too high for what? You do EM because you just built (part of) your system, and in doing so introduced clashes and non-ideal geometries. These lead to high potential energy, so you relax them with EM. What you see is how much the system relaxed. Noone usually cares how much potential energy was lost during EM. The thing that matters is whether the resulting system is relaxed enough to run the simulation. Cheers, Tsjerk On Sun, Apr 26, 2015 at 2:43 PM, Brett brettliu...@163.com wrote: Dear All, I just run the command gmx energy -f em.edr -o potential.xvg for my energy minimization step MD, but I find the RMSD given by this command is 142611, which I regard to be too high. Will you please explain to me what leads to the so high RMSD (Err.Est is 53000, Tot-Drift is -341107 KJ/mol)? I am looking forward to getting your reply. Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] a question related to gmx energy minimization
Dear All, I just run the command gmx energy -f em.edr -o potential.xvg for my energy minimization step MD, but I find the RMSD given by this command is 142611, which I regard to be too high. Will you please explain to me what leads to the so high RMSD (Err.Est is 53000, Tot-Drift is -341107 KJ/mol)? I am looking forward to getting your reply. Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] a question related to gmx energy minimization
Dear Justin, I mean why the RMSD is such huge. Does it mean in the energy mminimization step the protein has moved from point A to point B which is long long distance away from point A but, although the protein has been continously embedded in water? If the RMSD is above several thousands, it would mean the protein conformation after energy minimization would be absolutely different from the input pdb for the pdb2gmx. I am looking forward to getting a clarification. Brett At 2015-04-27 00:00:22, Justin Lemkul jalem...@vt.edu wrote: On 4/26/15 9:53 AM, Brett wrote: Dear Tsjerk, Will you please explain to me why the RMSD in this step is so large? For this reason I think there is something wrong. No, there's nothing wrong; the analysis in this case is meaningless. Energy minimization inherently makes large (orders of magnitude in many cases) changes to the potential as the structure is relaxed. An average energy over the course of this process has absolutely no physical meaning. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] the relationship between mdp file and the force field
Dear All, In the on-line Justin tutorial on lysozyme, the several mdp files are for the specific force field OPLS-AA force field. It specifically mentioned Settings, particularly nonbonded interaction settings, will be different for other force fields. Will you please introduce to me how to modify mdp files based on the difference of the force fields? For example, if I use force field 6, what should I modify based on the mdps of the lysozyme tutorial? I am looking forward to getting your reply. Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] pdb2gmx and protonated states of the residues
Dear All, By H++ and reduce we can have the input PDB for pdb2gmx have the initial corrected protonated states for some residues, for example, HIS, ARG, GLU and terminal residues. However biologically speaking with the change of the protein conformation, the protonated states of the above residues can be changed. Will you please introduce to me how GROMACS deal with the possible protonation state change during the MD process? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] how to name HIS in the input pdb for the pdb2gmx
Dear All， If we change HIS188 in Chain B to HISE188 in Chain B, before change the PDB looks like HIS B 188, but after change the PDB will look like HISEB 188, which makes thereis no space between HISE and Bchain. I do not know whether pdb2gmx can recognize HISEB 188, or we process it in some other way. I am looking forward to getting a reply from you. Brett At 2015-04-26 11:08:19, Justin Lemkul jalem...@vt.edu wrote: On 4/25/15 11:05 PM, Brett wrote: Dear All, For gromacs, for HIS residues there are HISD,HISE and HISH. In the original PDB file, are HIS residues are written as HIS. If based on necessity, I change exactly some HIS to HISD, some HIS to HISE and some HIS to HISH,the coordinate lines contaning HISD,HISE and HISH will not aling with all the other coordinate lines. Does pdb2gmx recognize these non-aligned coordinate lines? Or what other strategy you recommend me to take so that pdb2gmx can recognize HISD,HISE and HISH? Do the replacement properly and don't screw up column alignment. It needs to be correct for proper interpretation of the coordinates. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] how to name HIS in the input pdb for the pdb2gmx
Dear All, For gromacs, for HIS residues there are HISD,HISE and HISH. In the original PDB file, are HIS residues are written as HIS. If based on necessity, I change exactly some HIS to HISD, some HIS to HISE and some HIS to HISH,the coordinate lines contaning HISD,HISE and HISH will not aling with all the other coordinate lines. Does pdb2gmx recognize these non-aligned coordinate lines? Or what other strategy you recommend me to take so that pdb2gmx can recognize HISD,HISE and HISH? I am looking forward to getting your reply. Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] pdb2gmx on HID HIE and HIP
Dear All, Will you please tell me which software or server can handle a PDB file so that the HIS residues in the original PDB file will be automatically changed into HID, HIE and HIP in the new PDB file, which can be processed by pdb2gmx, based on the H patten in the HIS residues in the original PDB file? I am looking forward to getting your reply. Best regards. Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] pdb2gmx and the terminal residue
Dear All, For the pdb2gmx, if I will not assign charges to the N-terminal residue and C-terminal residue, I need to use pdb2gmx -ter, or I need to use pdb2gmx -[no]ter? In addition, whether there will be charges at the N-terminal residue and C-terminal residue has relation with the force field used, am I right? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] pdb2gmx and the Glu residue
Dear All, In the top file produced by H++ server for AMBER, if there is no charge for the Glu, the residue name will be modified to GLH. In our gromacs, we never treat Glu as without charge, thus we do not have GLH residue, am I right? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on regreressiontests
Dear All, For my installed gromacs, I just run the regression tests. It indicates PASSED but check mdp file differences, All 12 rotation tests PASSED, All o extra tests PASSED, All 42 pdb2gmx tests PASSED. Will you please advise whether I can use my installed gromacs without concern? What does it mean for PASSED but check mdp file differences? I am looking forward to getting your reply. Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] on the regression tests
Dear All, When I install gromacs-5.0.3, after the make check step, it indicates Regression tests have not been run. If you want to run them from the build systems,get the correct version of the regression tests ackage and set REGRESSION_PATH in CMake to point to it, or set REGRESSIONTEST_DOWNLOAF=ON. Without doing the regression tests, I complete the sudo make install and source /usr/local/gromacs/bin/GMXPC steps and completing the gromacs installation. Will you please let me know is any side-effect on my gromacs installation without the regression tests? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] definition of eigenvector in gromacs
Dear All, Recently I have read a gromacs related article which contain a sentence Trajectories pojected on the first two eigenvectors. Will you please tell me the meaning of eigenvector and Trajectories pojected on the first two eigenvectors? Will you please also explain it to me using common-used words simple as desk, meal, earth, etc? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] MD on protein-RNA complex
Dear Justin, What do you mean for Multi-chain and heterogeneous systems work out of the box? I am looking forward to getting your reply. Brett At 2015-03-04 10:50:10, Justin Lemkul jalem...@vt.edu wrote: On 3/3/15 9:34 PM, Brett wrote: Dear Justin, I mean is any difficulty or special for gromacs to recognize the RNA in the PDB file? Multi-chain and heterogeneous systems work out of the box. As with anything, the force field has to support everything and the nomenclature has to match the force field's expectations, but pdb2gmx will take care of everything. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] MD on protein-RNA complex
Dear All, Will you please introduce me a protocol on gromacs molecular dynamics simulation of protein-RNA complex? Brett -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
