[gmx-users] water in bulk
Dear All, Does Gromacs have a tool to calculate how many water molecules dissolve into the bulk of an organic solvent (let's say, 5 Angstrom from protein surface in the box)? Many thanks in advance. Regards, Jennifer -- 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] water in bulk
Dear Mark, Thanks a lot for the idea. I'll try. Regards, Jennifer On Wed, Jun 17, 2015 at 3:54 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, No, but you can use e.g. gmx select to describe a geometric criterion that you regard as equivalent to dissolve into bulk. If it finds atoms that satisfy, then that's your answer. Mark On Wed, Jun 17, 2015 at 2:44 PM Jennifer Vo quyvio...@gmail.com wrote: Dear All, Does Gromacs have a tool to calculate how many water molecules dissolve into the bulk of an organic solvent (let's say, 5 Angstrom from protein surface in the box)? Many thanks in advance. Regards, Jennifer -- 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] g_hbond on trajectory
Dear All, I used g_hbond to analyze the possible hydrogen bonds between protein and solvent (water) over the trajectory with this command: g_hbond -s md-1.tpr -f md.xtc -n index.ndx -hbm hbmap.xpm -num hbnum.xvg -g hbond.log -dist hbdist.xvg -nhbdist nhbdist.xvg The log file showed me: SER141OG SER141HG SOL2920OW SER141OG SER141HG SOL4449OW SER141OG SER141HG SOL5073OW SER141OG SER141HG SOL11886OW SER141OG SER141HG SOL13715OW I wonder if this calculation is based on one coordinate file (if yes, which one!?) or the average structure over trajectory? Many thanks in advance. Regards, Jennifer -- 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] g_hbond on trajectory
Thank you, Justin. Jennifer On Tue, Jun 2, 2015 at 2:09 PM, Justin Lemkul jalem...@vt.edu wrote: On 6/2/15 5:01 AM, Jennifer Vo wrote: Dear All, I used g_hbond to analyze the possible hydrogen bonds between protein and solvent (water) over the trajectory with this command: g_hbond -s md-1.tpr -f md.xtc -n index.ndx -hbm hbmap.xpm -num hbnum.xvg -g hbond.log -dist hbdist.xvg -nhbdist nhbdist.xvg The log file showed me: SER141OG SER141HG SOL2920OW SER141OG SER141HG SOL4449OW SER141OG SER141HG SOL5073OW SER141OG SER141HG SOL11886OW SER141OG SER141HG SOL13715OW I wonder if this calculation is based on one coordinate file (if yes, which one!?) or the average structure over trajectory? Trajectory analysis is done for every frame in the trajectory. The log output just indicates that different waters were hydrogen bonded to that particular Ser at different times. -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] Number Error in XTC file
Dear Mark, Many thanks for your answer. Is there anyway to overcome this? Regards, Jennifer On Tue, Apr 28, 2015 at 4:26 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, Typically that means you're reading a trajectory of size 2GB on a filesystem that can't do that (e.g. a 32-bit one). Mark On Tue, Apr 28, 2015 at 4:20 PM Jennifer Vo quyvio...@gmail.com wrote: Dear All, I have got the error in the end of trajectory converting: Magic Number Error in XTC file (read -335790888, should be 1995) trjconv -s md-1.tpr -f md-300ns-wat.xtc -o md_CA.pdb -n index_8pro.ndx -pbc mol -ur compact -center -skip 1000 Is there anybody know what`s the error about? Many thanks in advance. Jennifer -- 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] Number Error in XTC file
Dear All, I have got the error in the end of trajectory converting: Magic Number Error in XTC file (read -335790888, should be 1995) trjconv -s md-1.tpr -f md-300ns-wat.xtc -o md_CA.pdb -n index_8pro.ndx -pbc mol -ur compact -center -skip 1000 Is there anybody know what`s the error about? Many thanks in advance. Jennifer -- 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] Water TIP4Pnew and topology file
Dear Micholas , Many thanks for your recommendation. I have found the solution by replacing spc216.gro by tip4p.gro in gmx solvate. Regards, Jennifer On Wed, Apr 8, 2015 at 5:04 PM, Smith, Micholas D. smit...@ornl.gov wrote: How many ions did you add? You need to include in your .top file (after SOL) a line for each Ion type and the number of them. This needs to sum to 208074. Also make sure Ions.itp is included in your .top file === Micholas Dean Smith, PhD. Post-doctoral Research Associate University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Jennifer Vo quyvio...@gmail.com Sent: Wednesday, April 08, 2015 10:46 AM To: gmx-us...@gromacs.org Subject: [gmx-users] Water TIP4Pnew and topology file Dear Experts, I am dealing with this problem when trying to generate the .tpr file for adding Ions for the system. number of coordinates in coordinate file (1zk3_solvate.gro, 159792) does not match topology (topol.top, 208074) The system consits 4 chains of 4 proteins, 2 MG, uses Amber99SB ff and TIP4Pnew. The commands were: pdb2gmx -f 1ZK3_ABCD.pdb -p 1zk3.top -o 1zk3.gro editconf -f 1zk3.gro -o 1zk3_box.gro -bt cubic -d 1.2 -c gmx solvate -cp 1zk3_box.gro -cs spc216.gro -o 1zk3_solvate.gro -p topol.top grompp -f em_ion.mdp -c 1zk3_solvate.gro -p topol.top -o ions.tpr When I do cat 1zk3_solvate.gro | grep -c OW I have 48282 water molecules matching with topol.top file SOL 48282 Do you have any idea for a solution? Many thanks in advance. Regards, Jennifer -- 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] diisopropylethylene topology
Dear All, Does anyone has the itp file for diisopropylethylene? It would be very helpful if you can share. Many thanks in advance. Regards, Quy -- 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] g_rotacf and P 1,2,3 meaning
Dear All, When using g_rotacf, could you please explain to me the difference between option P 1, 2, and 3? The results from these are significantly different. Many thanks in advance. Regards, Jennifer -- 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 interpret g_principal output calculates
Dear All, I am trying to analyze how protein rotating in a mixture of organic solvent and water. I thought g_principal could help by checking the (xyz) of the whole protein over the time. The output gave 4 x.xvg files and I am not sure how to interpret them. Can I see the movement of protein by plotting the xyz vector? Many thanks in advance. Regards, Jennifer -- 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] why rotational correlation function decays to negative
Dear Tsjerk, Many thanks for a very clear answer! Regards, Jennifer On Wed, Mar 4, 2015 at 4:22 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Jennifer, The rotational autocorrelation looks at the correlation of the direction/extent of rotation as a function of time interval. The probability that it is going a certain way and still goes that direction a bit after is pretty large, so you get a positive correlation. A negative correlation means that, when you see it rotating one way at some time t, then, on average, you'll see it rotating the opposite direction after that interval of time. This may indicate that there are harmonic motions involved. Hope it helps, Tsjerk On Wed, Mar 4, 2015 at 11:01 AM, Jennifer Vo quyvio...@gmail.com wrote: Dear All, I calculated rotational correlation function by g_rotacf and saw the autocorrelation function started at 1 for t=0 and then decayed to 0 at t=35ns then continued to negative numbers (-0.2, -0.4, -0.5 at t-50ns). This is the command I use g_rotacf -s md_pro1_1st.tpr -n index.ndx -f md_pro1.xtc -o rotacf_pro1.xvg -P 1 This is the index.ndx [ C-alpha__r_76_r_93 ] 1076 1337 [ Backbone__r_76_r_93 ] 1074 1076 1086 1335 1337 1340 I try to calculate rotational correlation function of backbone and/or C_alpha (with -d in g_rotacf) between two residues 76 and 93 (the longest alpha helix in protein). So the negative number meant something wrong with my simulation or with the calculation? I would appreciate for any help. Regards, Jennifer -- 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.
Re: [gmx-users] solvate with an exact number of solvent molecules
Hi Rebeca, In GROMACS 5.0, I use gmx insert-molecules -f your.gro -ci your_insert.gro -o output.gro -nmol xxx where xxx is the number you want. Hope it helps. Jennifer On Mon, Mar 2, 2015 at 6:44 PM, Rebeca García Fandiño rega...@hotmail.com wrote: Dear GROMACS users, I am trying to do a systematic study using GROMACS and I would like to have the same number of solvent molecules in all my systems. Using gmx solvate in GROMACS 5.0 it is only possible to select the maximum number of molecules in the box, but not a concrete number. Does anyone knows about any way to solvate a molecule selecting an exact number of solvent molecules in the box? Thanks a lot in advance. Best wishes, Rebeca. Dr. Rebeca Garcia Santiago de Compostela University Spain -- 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] multiple ligands topology
Dear Justin, I did the whole procedure again with protein and one ligand by one and then with two ligands and have found the problem due to the overriding. Many thanks for all of your valuable helps! Regards, Jennifer On Mon, Feb 16, 2015 at 1:41 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/16/15 3:49 AM, Jennifer Vo wrote: Dear Justin, Many thanks again. I just define a small box then insert molecules and let it floating nearby the protein, then redefine the actual box for the real concentration of protein. The maxwarn 27 is from this NOTE 1 [file em_ion.mdp]: With Verlet lists the optimal nstlist is = 10, with GPUs = 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to 2002995045 WARNING 1 [file my_ligand_atomtypes.itp, line 3]: Overriding atomtype CA WARNING 2 [file my_ligand_atomtypes.itp, line 4]: Overriding atomtype H4 WARNING 3 [file my_ligand_atomtypes.itp, line 5]: Overriding atomtype HA WARNING 4 [file my_ligand_atomtypes.itp, line 6]: Overriding atomtype C WARNING 5 [file my_ligand_atomtypes.itp, line 7]: Overriding atomtype O WARNING 6 [file my_ligand_atomtypes.itp, line 8]: Overriding atomtype N WARNING 7 [file my_ligand_atomtypes.itp, line 9]: Overriding atomtype H WARNING 8 [file my_ligand_atomtypes.itp, line 10]: Overriding atomtype N* WARNING 9 [file my_ligand_atomtypes.itp, line 11]: Overriding atomtype CT WARNING 10 [file my_ligand_atomtypes.itp, line 12]: Overriding atomtype H2 WARNING 11 [file my_ligand_atomtypes.itp, line 13]: Overriding atomtype H1 WARNING 12 [file my_ligand_atomtypes.itp, line 14]: Overriding atomtype OH WARNING 13 [file my_ligand_atomtypes.itp, line 15]: Overriding atomtype HO WARNING 14 [file my_ligand_atomtypes.itp, line 16]: Overriding atomtype OS WARNING 15 [file my_ligand_atomtypes.itp, line 17]: Overriding atomtype P WARNING 16 [file my_ligand_atomtypes.itp, line 18]: Overriding atomtype O2 WARNING 17 [file my_ligand_atomtypes.itp, line 19]: Overriding atomtype CK WARNING 18 [file my_ligand_atomtypes.itp, line 20]: Overriding atomtype H5 WARNING 19 [file my_ligand_atomtypes.itp, line 21]: Overriding atomtype NB WARNING 20 [file my_ligand_atomtypes.itp, line 22]: Overriding atomtype CB WARNING 21 [file my_ligand_atomtypes.itp, line 23]: Overriding atomtype N2 WARNING 22 [file my_ligand_atomtypes.itp, line 24]: Overriding atomtype NC WARNING 23 [file my_ligand_atomtypes.itp, line 25]: Overriding atomtype CQ Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'A' Excluding 3 bonded neighbours molecule type 'B' Excluding 3 bonded neighbours molecule type 'NPD' Excluding 3 bonded neighbours molecule type 'IR3' Excluding 2 bonded neighbours molecule type 'SOL' And I think it's harmless to ignore the warning here for the overriding atomtype. Am I correct? The image of ligand is in the link Well, if you're overriding atom types, that means you're potentially changing elements of the force field. That can cause catastrophic problems if you're not careful. If these types are simply re-defining the same parameters already in the force field, then yes it is safe, but also inherently unnecessary. http://postimg.org/image/fojbmkhrb/ Some of these ligands have extremely bizarre geometries, with H overlapping heavy atoms. Something looks very wrong. -Justin I would really appreciate for a help. Regards, Jennifer On Fri, Feb 13, 2015 at 10:45 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/13/15 2:47 PM, Jennifer Vo wrote: Dear Justin, Please find the figure of output pdb file after minimizatrion.(I have sent in the previous email but it's pending... So I send it again) The list doesn't accept attachments (if I had a nickel for every time I said that...) so if you want to share images, upload them to a file-sharing service and post the URL. Here is step by step how I built the system ### concatenate 2 chains and renumber the residues genconf -f AB.gro -o AB_renumber.gro -renumber ### redefine the small box the the proteins editconf -f AB_renumber.gro -o AB_box.gro -bt cubic -d 0.5 -c ### insert the first ligand gmx insert-molecules -f AB_box.gro -ci ligand1.gro -o AB_NADPH.pdb -nmol 1 ### insert the second ligand gmx insert-molecules -f AB_NADPH.pdb -ci ir3_em.gro -o AB_NADPH_IR3.pdb -nmol 9 -seed -1 OK, so ligands are actually just randomly inserted molecules, freely floating in the solvent. ### redefine the box the the system editconf -f AB_NADPH_IR3.pdb -o AB_NADPH_IR3_box.pdb -bt cubic -d 1.0 -c Why is this necessary? ### adding water gmx solvate -cp AB_NADPH_IR3_box.pdb -cs spc216.gro -o
[gmx-users] multiple ligands topology
Dear All, I am running a simulation for a systems including two chains of proteins and two ligands using amber 99SB ff. My topol.top is #include amber99sb.ff/forcefield.itp #include my_ligand_atomtypes.itp ; Include chain topologies #include A.itp #ifdef POSRES #include posre_A.itp #endif #include B.itp #ifdef POSRES #include posre_B.itp #endif ; Include custom ligand topologies #include npd.itp #ifdef POSRES_LIG #include posre_npd.itp #endif ; Include custom ligand topologies #include ir3_em.itp ; Include water topology #include amber99sb.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic ion topology #include amber99sb.ff/ions.itp [ system ] ; Name BcSIRED in water [ molecules ] ; Compound#mols A 1 B 1 NPD 1 IR3 9 SOL 123406 NA 24 then I have my_ligand_atomtypes.itp [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb CA CA 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H4 H4 0.0 0.0 A 2.51055e-01 6.27600e-02 ; 1.41 0.0150 HA HA 0.0 0.0 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 CC 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 OO 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 NN 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 HH 0.0 0.0 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 N* N* 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CT CT 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 H2 H2 0.0 0.0 A 2.29317e-01 6.56888e-02 ; 1.29 0.0157 H1 H1 0.0 0.0 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157 OH OH 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 HO HO 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. OS OS 0.0 0.0 A 3.1e-01 7.11280e-01 ; 1.68 0.1700 PP 0.0 0.0 A 3.74177e-01 8.36800e-01 ; 2.10 0.2000 O2 O2 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 CK CK 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H5 H5 0.0 0.0 A 2.42146e-01 6.27600e-02 ; 1.36 0.0150 NB NB 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CB CB 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 N2 N2 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 NC NC 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CQ CQ 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 ; IR3_GMX.top created by acpype (Rev: 403) on Wed Feb 4 11:55:46 2015 ; Include forcefield parameters [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb CC 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 HH 0.0 0.0 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 NN 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 My first ligand gro file GRoups of Organic Molecules in ACtion for Science 73 1NPD OA221 -0.282 0.251 -5.719 1NPD OA232 -0.142 0.366 -5.542 1NPD OA243 -0.039 0.314 -5.771 1NPD P'A24 -0.145 0.285 -5.669 1NPD PA5 -0.033 -0.056 -5.010 1NPD PN6 -0.130 -0.245 -4.804 1NPDO3P7 -0.126 -0.116 -4.893 1NPDN1A8 -0.692 0.110 -5.840 1NPDN1N9 -0.539 -0.355 -4.443 1NPDC2A 10 -0.613 0.000 -5.836 ... 1NPDH8A 73 -0.376 0.292 -5.440 1.94588 0.88647 1.08377 My second ligand gro file IR3_GMX.gro created by acpype (Rev: 403) on Wed Feb 4 11:55:46 2015 22 1IR3CAA1 10.182 10.576 10.387 1IR3HAB2 10.211 10.640 10.305 1IR3HAA3 10.075 10.577 10.396 1IR3HAF 22 10.581 10.138 10.385 20.72517 20.72517 20.72517 but the system can`t go under energy minimization. This is my em.mdp title = Minimization ; Title of run integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 1000.0; Stop minimization when the maximum force 1000.0 kJ/mol emstep = 0.01 ; Energy step size nsteps = 50; Maximum number of (minimization) steps to perform energygrps = Protein NPD IR3
Re: [gmx-users] multiple ligands topology
Dear Justin, Many thanks for your kind answer. The output of minimization for Protein + 1 Ligand Steepest Descents converged to Fmax 100 in 868 steps Potential Energy = -8.0409740e+06 Maximum force = 8.3073639e+01 on atom 267747 Norm of force = 3.5544858e+00 The out for Protein + 2 ligands Steepest Descents converged to Fmax 100 in 2165 steps Potential Energy = -6.2125650e+06 Maximum force = 8.6047729e+01 on atom 263858 Norm of force = 3.6529241e+00 I don't see any failure. But when I use trjconv from Output gro file to pdb file, I see the ligands screwed up. In case The ligand files are both set up within different boxes, so perhaps the construction of your system is incorrect somehow, how do I fix it? Do I have to change the final line of every ligand's topology file? Which are 1IR3HAF 22 10.581 10.138 10.385 20.72517 20.72517 20.72517 and 1NPDH8A 73 -0.376 0.292 -5.440 1.94588 0.88647 1.08377 and the box of the System including Proteins + 2 ligands 23746NA NA79296 15.582 10.741 1.636 15.63000 15.63000 15.63000 Many thanks in advance! Jennifer On Fri, Feb 13, 2015 at 3:44 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/13/15 6:03 AM, Jennifer Vo wrote: Dear All, I am running a simulation for a systems including two chains of proteins and two ligands using amber 99SB ff. My topol.top is #include amber99sb.ff/forcefield.itp #include my_ligand_atomtypes.itp ; Include chain topologies #include A.itp #ifdef POSRES #include posre_A.itp #endif #include B.itp #ifdef POSRES #include posre_B.itp #endif ; Include custom ligand topologies #include npd.itp #ifdef POSRES_LIG #include posre_npd.itp #endif ; Include custom ligand topologies #include ir3_em.itp ; Include water topology #include amber99sb.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic ion topology #include amber99sb.ff/ions.itp [ system ] ; Name BcSIRED in water [ molecules ] ; Compound#mols A 1 B 1 NPD 1 IR3 9 SOL 123406 NA 24 then I have my_ligand_atomtypes.itp [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb CA CA 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H4 H4 0.0 0.0 A 2.51055e-01 6.27600e-02 ; 1.41 0.0150 HA HA 0.0 0.0 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 CC 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 OO 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 NN 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 HH 0.0 0.0 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 N* N* 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CT CT 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 H2 H2 0.0 0.0 A 2.29317e-01 6.56888e-02 ; 1.29 0.0157 H1 H1 0.0 0.0 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157 OH OH 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 HO HO 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. OS OS 0.0 0.0 A 3.1e-01 7.11280e-01 ; 1.68 0.1700 PP 0.0 0.0 A 3.74177e-01 8.36800e-01 ; 2.10 0.2000 O2 O2 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 CK CK 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H5 H5 0.0 0.0 A 2.42146e-01 6.27600e-02 ; 1.36 0.0150 NB NB 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CB CB 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 N2 N2 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 NC NC 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CQ CQ 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 ; IR3_GMX.top created by acpype (Rev: 403) on Wed Feb 4 11:55:46 2015 ; Include forcefield parameters [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb CC 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 HH 0.0 0.0 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 NN 0.0 0.0 A 3.25000e-01 7.11280e-01
Re: [gmx-users] multiple ligands topology
Dear Justin, Please find the figure of output pdb file after minimizatrion.(I have sent in the previous email but it's pending... So I send it again) Here is step by step how I built the system ### concatenate 2 chains and renumber the residues genconf -f AB.gro -o AB_renumber.gro -renumber ### redefine the small box the the proteins editconf -f AB_renumber.gro -o AB_box.gro -bt cubic -d 0.5 -c ### insert the first ligand gmx insert-molecules -f AB_box.gro -ci ligand1.gro -o AB_NADPH.pdb -nmol 1 ### insert the second ligand gmx insert-molecules -f AB_NADPH.pdb -ci ir3_em.gro -o AB_NADPH_IR3.pdb -nmol 9 -seed -1 ### redefine the box the the system editconf -f AB_NADPH_IR3.pdb -o AB_NADPH_IR3_box.pdb -bt cubic -d 1.0 -c ### adding water gmx solvate -cp AB_NADPH_IR3_box.pdb -cs spc216.gro -o AB_NADPH_IR3_solvate.pdb -p topol.top ### convert pdb to gro file editconf -f AB_NADPH_IR3_solvate.pdb -o AB_NADPH_IR3_solvate.gro ### adding ions grompp -f em_ion.mdp -c AB_NADPH_IR3_solvate.gro -p topol.top -o ions.tpr -maxwarn 27 genion -s ions.tpr -o AB_NADPH_IR3_solvate_ions.gro -p topol.top -pname NA -np 24 -n index.ndx Many thanks for your help. On Fri, Feb 13, 2015 at 4:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/13/15 9:59 AM, Jennifer Vo wrote: Dear Justin, Many thanks for your kind answer. The output of minimization for Protein + 1 Ligand Steepest Descents converged to Fmax 100 in 868 steps Potential Energy = -8.0409740e+06 Maximum force = 8.3073639e+01 on atom 267747 Norm of force = 3.5544858e+00 The out for Protein + 2 ligands Steepest Descents converged to Fmax 100 in 2165 steps Potential Energy = -6.2125650e+06 Maximum force = 8.6047729e+01 on atom 263858 Norm of force = 3.6529241e+00 I don't see any failure. But when I use trjconv from Output gro file to pdb file, I see the ligands screwed up. Again, please define what this means. How did you build the system? Can you share an image? In case The ligand files are both set up within different boxes, so perhaps the construction of your system is incorrect somehow, how do I fix it? Do I have to change the final line of every ligand's topology file? Well, assuming you're copying and pasting coordinates to construct the system, if they're defined in different boxes, they're probably not going to be where they should be when you define a third box with different dimensions, unless you're using editconf to reposition in between. Again, you'll need to provide actual specifics of how you built the system (step-by-step commands, please). -Justin Which are 1IR3HAF 22 10.581 10.138 10.385 20.72517 20.72517 20.72517 and 1NPDH8A 73 -0.376 0.292 -5.440 1.94588 0.88647 1.08377 and the box of the System including Proteins + 2 ligands 23746NA NA79296 15.582 10.741 1.636 15.63000 15.63000 15.63000 Many thanks in advance! Jennifer On Fri, Feb 13, 2015 at 3:44 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/13/15 6:03 AM, Jennifer Vo wrote: Dear All, I am running a simulation for a systems including two chains of proteins and two ligands using amber 99SB ff. My topol.top is #include amber99sb.ff/forcefield.itp #include my_ligand_atomtypes.itp ; Include chain topologies #include A.itp #ifdef POSRES #include posre_A.itp #endif #include B.itp #ifdef POSRES #include posre_B.itp #endif ; Include custom ligand topologies #include npd.itp #ifdef POSRES_LIG #include posre_npd.itp #endif ; Include custom ligand topologies #include ir3_em.itp ; Include water topology #include amber99sb.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic ion topology #include amber99sb.ff/ions.itp [ system ] ; Name BcSIRED in water [ molecules ] ; Compound#mols A 1 B 1 NPD 1 IR3 9 SOL 123406 NA 24 then I have my_ligand_atomtypes.itp [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb CA CA 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H4 H4 0.0 0.0 A 2.51055e-01 6.27600e-02 ; 1.41 0.0150 HA HA 0.0 0.0 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 CC 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 OO 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 NN 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 HH 0.0 0.0 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 N* N* 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CT
Re: [gmx-users] topology and parameter set up
Dear Justin, Many thanks for your help. My em.mdp is integrator = steep emtol = 100.0 emstep = 0.01 nsteps = 10 coulombtype = PME pbc = xyz My nvt.mdp is title = Protein-ligand complex NVT equilibration define = -DPOSRES -DPOSRES_LIG ; position restrain the protein and ligand ; Run parameters integrator = md; leap-frog integrator nsteps = 5 ; 2 * 5 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 500 ; save coordinates every 1.0 ps nstvout = 500 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps energygrps = Protein NPD ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = hbonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10; 20 fs, largely irrelevant with Verlet rcoulomb= 1.4 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein_NPD Water_and_ions; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed It generated no error in the log file. This is em.log Steepest Descents converged to Fmax 100 in 10536 steps Potential Energy = -2.1753502e+06 Maximum force = 8.4056786e+01 on atom 12 Norm of force = 4.0102091e+00 For the NPT.mdp, since I have got error from the previous run, so I tried commenting out the neighborsearching part to take the default number and there is still error as the previous email. Regarding the coordinates, I merged 2 coordinate files into 1 file as your tutorial about Protein-Ligand Simulation ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html) and run a genconf to renumber the system, editconf to create the cubic box and genbox to solvate the system. Then I add 24 NA since the charge of the whole system is -24. I don't know which step is a possible cause to the error. Regards, Jennifer On Mon, Feb 2, 2015 at 1:57 PM, Justin Lemkul jalem...@vt.edu wrote: On 2/2/15 6:37 AM, Jennifer Vo wrote: Dear Experts, I am facing the problem of simulation of protein - ligand complex using amber99sb force field. Since I created a topol.top for the system ; Include forcefield parameters #include amber99sb.ff/forcefield.itp [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb CA CA 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H4 H4 0.0 0.0 A 2.51055e-01 6.27600e-02 ; 1.41 0.0150 HA HA 0.0 0.0 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 CC 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 OO 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 NN 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 HH 0.0 0.0 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 N* N* 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CT CT 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 H2 H2 0.0 0.0 A 2.29317e-01 6.56888e-02 ; 1.29 0.0157 H1 H1 0.0 0.0 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157 OH OH 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 HO HO 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. OS OS 0.0 0.0 A 3.1e-01 7.11280e-01 ; 1.68 0.1700 PP 0.0 0.0
[gmx-users] topology and parameter set up
Dear Experts, I am facing the problem of simulation of protein - ligand complex using amber99sb force field. Since I created a topol.top for the system ; Include forcefield parameters #include amber99sb.ff/forcefield.itp [ atomtypes ] ;name bond_type mass charge ptype sigma epsilon Amb CA CA 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H4 H4 0.0 0.0 A 2.51055e-01 6.27600e-02 ; 1.41 0.0150 HA HA 0.0 0.0 A 2.59964e-01 6.27600e-02 ; 1.46 0.0150 CC 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 OO 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 NN 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 HH 0.0 0.0 A 1.06908e-01 6.56888e-02 ; 0.60 0.0157 N* N* 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CT CT 0.0 0.0 A 3.39967e-01 4.57730e-01 ; 1.91 0.1094 H2 H2 0.0 0.0 A 2.29317e-01 6.56888e-02 ; 1.29 0.0157 H1 H1 0.0 0.0 A 2.47135e-01 6.56888e-02 ; 1.39 0.0157 OH OH 0.0 0.0 A 3.06647e-01 8.80314e-01 ; 1.72 0.2104 HO HO 0.0 0.0 A 0.0e+00 0.0e+00 ; 0.00 0. OS OS 0.0 0.0 A 3.1e-01 7.11280e-01 ; 1.68 0.1700 PP 0.0 0.0 A 3.74177e-01 8.36800e-01 ; 2.10 0.2000 O2 O2 0.0 0.0 A 2.95992e-01 8.78640e-01 ; 1.66 0.2100 CK CK 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 H5 H5 0.0 0.0 A 2.42146e-01 6.27600e-02 ; 1.36 0.0150 NB NB 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CB CB 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 N2 N2 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 NC NC 0.0 0.0 A 3.25000e-01 7.11280e-01 ; 1.82 0.1700 CQ CQ 0.0 0.0 A 3.39967e-01 3.59824e-01 ; 1.91 0.0860 ; Include chain topologies #include A.itp ; Include Position restraint file #ifdef POSRES #include posre_A.itp #endif ; Include chain topologies #include B.itp ; Include Position restraint file #ifdef POSRES #include posre_B.itp #endif ; Include custom ligand topologies #include npd.itp ; Ligand position restraints #ifdef POSRES_LIG #include posre_npd.itp #endif ; Include water topology #include amber99sb.ff/tip3p.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic ion topology #include amber99sb.ff/ions.itp [ system ] ; Name system in water [ molecules ] ; Compound#mols A 1 B 1 NPD 1 SOL 42322 NA 24 The Protein and the Ligand were under energy minimization and a short MD separatedly to be sure there is no problem with the topology. But when I merge two topol.top from protein and from ligand, the error came at NPT step after successfully energy minimization and NVT This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. This is NPT.mdp title = system in water define = -DPOSRES -DPOSRES_LIG ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps = 50; 2 * 50 = 1000 ps, 1 ns dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 1.0 ps nstvout = 5000 ; save velocities every 1.0 ps nstenergy = 500 ; save energies every 1.0 ps nstlog = 500 ; update log file every 1.0 ps energygrps = Protein NPD ; Bond parameters continuation= yes ; Restarting after NVT constraint_algorithm= lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ;
Re: [gmx-users] Atomtype P,SI not found from grompp
Dear Justin, Thanks a lot. I tried to use all of the NADPH from ATB ( http://compbio.biosci.uq.edu.au/atb/index.py) and they have the same problem. Regarding the P, SI, ist atom type P, SI (with one space in between) is existed in the gromos 54A7 force field #define ga_26 120.00 530.00 ; P, SI - OA - CHn, P 95 in file gromos54a7.ff/ffbonded.itp. It means it's not a new atom type, did I interpret correctly? Regards, Jennifer On Fri, Jan 23, 2015 at 5:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/23/15 9:52 AM, Jennifer Vo wrote: Dear Justin, I did try replacing the P,SI to P but the ligand was distorted during energy minimization (error happened excactly at the position of P). Then I tried replacing P,SI to P, SI (with one space in between) according to the existed gromos54a7 force field but got the error when running grompp: *Too few parameters on line (62) * which is the line of 3 P, SI as following: ; nr type resnr resid atom cgnr chargemasstotal_charge 1OA1NAP O1X1 -0.797 15.9994 2 H1NAP H410.295 1.0080 ; -0.502 3 P, SI1NAP P2B22.585 30.9738 4OM1NAP O3X2 -1.083 15.9994 5OA1NAP O2X2 -0.797 15.9994 Keep playing around by replacing P, SI with PSI on all files but it also didn't work, Could you please help me for a solution in this case? If the parameters provided distort the structure, you need to find or derive better ones. You can't sub in nonsensical atom types and hope for it to work :) -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] Atomtype P,SI not found from grompp
Dear Justin, Now I get it. Thanks a lot for taking your time. I sent the email to the author of ATB developer and still waiting for the answer. Many thanks again. Regards, Jennifer On Fri, Jan 23, 2015 at 5:54 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/23/15 11:51 AM, Jennifer Vo wrote: Dear Justin, Thanks a lot. I tried to use all of the NADPH from ATB ( http://compbio.biosci.uq.edu.au/atb/index.py) and they have the same problem. Regarding the P, SI, ist atom type P, SI (with one space in between) is existed in the gromos 54A7 force field #define ga_26 120.00 530.00 ; P, SI - OA - CHn, P 95 in file gromos54a7.ff/ffbonded.itp. It means it's not a new atom type, did I interpret correctly? No. The comment does not tell you that P,SI is an atom type. It tells you that the angle parameter there is applicable to either P or SI in the first position (atom i), OA in the second position (atom j), then either CHn or P in the last position (atom k). The available atom types for the force field are in atomtypes.atp. If it's not there, it's not real. I recall our previous discussions about the source of the topology. Hopefully you have alerted the ATB developers to the erroneous topology that they're distributing. If your atom is a phosphorus, the atom type is P. Don't change it. If the parameters are sub-par, then derive new ones or choose a better force field. -Justin Regards, Jennifer On Fri, Jan 23, 2015 at 5:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/23/15 9:52 AM, Jennifer Vo wrote: Dear Justin, I did try replacing the P,SI to P but the ligand was distorted during energy minimization (error happened excactly at the position of P). Then I tried replacing P,SI to P, SI (with one space in between) according to the existed gromos54a7 force field but got the error when running grompp: *Too few parameters on line (62) * which is the line of 3 P, SI as following: ; nr type resnr resid atom cgnr chargemasstotal_charge 1OA1NAP O1X1 -0.797 15.9994 2 H1NAP H410.295 1.0080 ; -0.502 3 P, SI1NAP P2B22.585 30.9738 4OM1NAP O3X2 -1.083 15.9994 5OA1NAP O2X2 -0.797 15.9994 Keep playing around by replacing P, SI with PSI on all files but it also didn't work, Could you please help me for a solution in this case? If the parameters provided distort the structure, you need to find or derive better ones. You can't sub in nonsensical atom types and hope for it to work :) -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. -- == 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] Atomtype P,SI not found from grompp
Dear Justin, I did try replacing the P,SI to P but the ligand was distorted during energy minimization (error happened excactly at the position of P). Then I tried replacing P,SI to P, SI (with one space in between) according to the existed gromos54a7 force field but got the error when running grompp: *Too few parameters on line (62) * which is the line of 3 P, SI as following: ; nr type resnr resid atom cgnr chargemasstotal_charge 1OA1NAP O1X1 -0.797 15.9994 2 H1NAP H410.295 1.0080 ; -0.502 3 P, SI1NAP P2B22.585 30.9738 4OM1NAP O3X2 -1.083 15.9994 5OA1NAP O2X2 -0.797 15.9994 Keep playing around by replacing P, SI with PSI on all files but it also didn't work, Could you please help me for a solution in this case? Many thanks in advance. Regards, Jennifer On Thu, Jan 15, 2015 at 10:43 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/15/15 1:58 PM, Jennifer Vo wrote: Dear Justin, Thanks again! I have downloaded the topology from Automated Topology Builder (http://compbio.chemistry.uq.edu.au/atb/index.py) using the existing molecules. Checking all of the *.itp file with both GROMOS 54A7 and GROMOS 534A6 force field for all of the NADPH they provided, I see all of these have the P,SI type. I would like to ask for your advice in this case. Sounds like an error to me. Distributing topologies that trigger fatal errors is probably not what they intended, so I suggest you make them aware of this problem. P and SI have the same nonbonded parameters, so you're safe to simply replace the P,SI with the proper atom type in this case. -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] Atoms in the .top are not numbered consecutively from 1
Dear All, I have got this error after running grompp Fatal error: Atoms in the .top are not numbered consecutively from 1 (rather, atomnr = 4, while at-nr = 2) My topology file is ; Include forcefield parameters #include gromos54a7.ff/forcefield.itp ; Include ligand topology #include nap_uniatom.itp ; Include water topology #include gromos54a7.ff/spc.itp ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif [ system ] ; Name NAP in water [ molecules ] ; Compound#mols NAP 1 SOL 2654 The I checked the file nap_uniatom.itp and it start from Atom 1, NAP 8026 1NAPO3X1 2.599 2.617 1.841 1NAP HOP32 2.518 2.642 1.886 1NAPP2B3 2.654 2.469 1.866 1NAPO1X4 2.628 2.363 1.772 1NAPO2B5 2.580 2.447 2.009 1NAPO2X6 2.802 2.504 1.908 1NAP HOP27 2.817 2.591 1.946 Could you please tell me where is the problem from and a possible solution? Many thanks in advance. Regards, Jennifer -- 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] Atoms in the .top are not numbered consecutively from 1
Dear All, Sorry for pasting the *.gro file instead of topology. Here is the topology [ moleculetype ] ; Name nrexcl NAP 3 [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1OA1NAP O3X1 -0.796 15.9994 2 H1NAPHOP310.297 1.0080 3 P, SI1NAP P2B12.683 30.9738 4OM1NAP O1X1 -1.000 15.9994 5OA1NAP O2B1 -0.685 15.9994 6OA1NAP O2X1 -0.796 15.9994 It starts from 1 as well. Many thanks for any help. Regards, Jennifer On Fri, Jan 23, 2015 at 5:13 PM, Jennifer Vo quyvio...@gmail.com wrote: Dear All, I have got this error after running grompp Fatal error: Atoms in the .top are not numbered consecutively from 1 (rather, atomnr = 4, while at-nr = 2) My topology file is ; Include forcefield parameters #include gromos54a7.ff/forcefield.itp ; Include ligand topology #include nap_uniatom.itp ; Include water topology #include gromos54a7.ff/spc.itp ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif [ system ] ; Name NAP in water [ molecules ] ; Compound#mols NAP 1 SOL 2654 The I checked the file nap_uniatom.itp and it start from Atom 1, NAP 8026 1NAPO3X1 2.599 2.617 1.841 1NAP HOP32 2.518 2.642 1.886 1NAPP2B3 2.654 2.469 1.866 1NAPO1X4 2.628 2.363 1.772 1NAPO2B5 2.580 2.447 2.009 1NAPO2X6 2.802 2.504 1.908 1NAP HOP27 2.817 2.591 1.946 Could you please tell me where is the problem from and a possible solution? Many thanks in advance. Regards, Jennifer -- 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] Too many LINCS warnings
Dear Experts, I am running an nvt equilibration for a System including 2 Proteins and 2 ligands. I have got this error: *Fatal error:Too many LINCS warnings (1000)If you know what you are doing you can adjust the lincs warning threshold in your mdp fileor set the environment variable GMX_MAXCONSTRWARN to -1,but normally it is better to fix the problem* Reading from some forums I thought it could be (1) the system was insufficiently minimized, (2) the .mdp settings are incorrect, and/or (3) the ligand topology is flawed. I checked the potential energy after EM and the pdb file, it looks stable and fine to me. I guess my nvt.mdp file is incorrect (please find them in attachments). Could you please guide me where is the incorrect point? Many thanks for any help. Regards, Jennifer -- 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] Atomtype P,SI not found from grompp
Dear Justin, Many thanks. It's clear to me now. I will contact them for this issue. Regards, Jennifer On Thu, Jan 15, 2015 at 10:43 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/15/15 1:58 PM, Jennifer Vo wrote: Dear Justin, Thanks again! I have downloaded the topology from Automated Topology Builder (http://compbio.chemistry.uq.edu.au/atb/index.py) using the existing molecules. Checking all of the *.itp file with both GROMOS 54A7 and GROMOS 534A6 force field for all of the NADPH they provided, I see all of these have the P,SI type. I would like to ask for your advice in this case. Sounds like an error to me. Distributing topologies that trigger fatal errors is probably not what they intended, so I suggest you make them aware of this problem. P and SI have the same nonbonded parameters, so you're safe to simply replace the P,SI with the proper atom type in this case. -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] Atomtype P,SI not found from grompp
Dear Justin, Thanks a lot, now I got it. I thought P and SI is the two separated atoms so I searched for them two times. Now the grep P,SI *.* returned nap_allatom.itp:3 P,SI1NAPP2B12.247 30.9738 nap_allatom.itp: 21 P,SI1NAP PA42.315 30.9738 nap_allatom.itp: 26 P,SI1NAP PN52.259 30.9738 should I change P,SI to P only? Regards, Jennifer On Thu, Jan 15, 2015 at 7:08 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/15/15 12:57 PM, Jennifer Vo wrote: Dear Justin, Many thanks for your answer. I tried grep SI *.* That won't return anything if what you posted before was accurate. The atomtype in question was P,SI unless you modified the error message. grepping for SI (e.g. with a space on either side of it) won't match P,SI in anything. -Justin in the whole working directory but nothing found. Where could it be if I have to search? Thanks a lot again. Regards, Jennifer On Thu, Jan 15, 2015 at 6:44 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/15/15 12:20 PM, Jennifer Vo wrote: Dear Experts, I ran a grompp (gromos53a6 ff) grompp -f em.mdp -c complex2_solvated.gro -p topol.top -o complex.tpr and it generated the error Atomtype P,SI not found I checked the gromos53a6.ff/atomtypes.atp and see there are P, SI in the list SI 28.08; Silicon P 30.97380 ; Phosphor And there is no P, SI in my complex2_solvated.gro file! I really do appreciate for any help. It's an atom type, so it won't be in a coordinate file. Something in a topology or force field file is specifying something called P,SI as an atomtype. That's clearly not sensible. -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. -- == 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] Atomtype P,SI not found from grompp
Dear Justin, Thanks again! I have downloaded the topology from Automated Topology Builder (http://compbio.chemistry.uq.edu.au/atb/index.py) using the existing molecules. Checking all of the *.itp file with both GROMOS 54A7 and GROMOS 534A6 force field for all of the NADPH they provided, I see all of these have the P,SI type. I would like to ask for your advice in this case. Regards, Jennifer On Thu, Jan 15, 2015 at 7:37 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/15/15 1:31 PM, Jennifer Vo wrote: Dear Justin, Thanks a lot, now I got it. I thought P and SI is the two separated atoms so I searched for them two times. Now the grep P,SI *.* returned nap_allatom.itp:3 P,SI1NAPP2B12.247 30.9738 nap_allatom.itp: 21 P,SI1NAP PA42.315 30.9738 nap_allatom.itp: 26 P,SI1NAP PN52.259 30.9738 should I change P,SI to P only? If the atom name is an indicator of what the atom is, then presumably yes. But I would be wary of any topology in general that used nonsense atom types in the parameters it produces, unless there is some additional (external) set of parameters upon which this molecule relies, e.g. something that defines new parameters and interactions for something called P,SI. -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] Atomtype P,SI not found from grompp
Dear Experts, I ran a grompp (gromos53a6 ff) grompp -f em.mdp -c complex2_solvated.gro -p topol.top -o complex.tpr and it generated the error Atomtype P,SI not found I checked the gromos53a6.ff/atomtypes.atp and see there are P, SI in the list SI 28.08; Silicon P 30.97380 ; Phosphor And there is no P, SI in my complex2_solvated.gro file! I really do appreciate for any help. Regards, Jennifer -- 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] Atomtype P,SI not found from grompp
Dear Justin, Many thanks for your answer. I tried grep SI *.* in the whole working directory but nothing found. Where could it be if I have to search? Thanks a lot again. Regards, Jennifer On Thu, Jan 15, 2015 at 6:44 PM, Justin Lemkul jalem...@vt.edu wrote: On 1/15/15 12:20 PM, Jennifer Vo wrote: Dear Experts, I ran a grompp (gromos53a6 ff) grompp -f em.mdp -c complex2_solvated.gro -p topol.top -o complex.tpr and it generated the error Atomtype P,SI not found I checked the gromos53a6.ff/atomtypes.atp and see there are P, SI in the list SI 28.08; Silicon P 30.97380 ; Phosphor And there is no P, SI in my complex2_solvated.gro file! I really do appreciate for any help. It's an atom type, so it won't be in a coordinate file. Something in a topology or force field file is specifying something called P,SI as an atomtype. That's clearly not sensible. -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] trjconv mismatch
Dear All, I have got this error while running trjconv from .xtc to .pdb file. The System includes 8 Protein (4622 Atoms each, x8 = 36976 Atoms). 135978 is the total number of Atoms in the System. The index.ndx was created from md.gro file, and I Chose #1 for Protein. I don't know where is the original error of the mismatch here Fatal error: Index[4622] 135978 is larger than the number of atoms in the trajectory file (36976). There is a mismatch in the contents of your -f, -s and/or -n files. I would appreciate for any help. Jennifer. -- 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] trjconv mismatch
Dear Mark, Many thanks for your reply. My command was: trjconv_mpi -f md-*.trr -n index.ndx -timestep 100 -o md-*-timestep100.xtc for every trr file, then concatenate by using trjcat_mpi -f md-*-timestep100.xtc -n index.ndx -o md-timestep100.xtc For index.ndx: make_ndx_mpi -f md.gro -o index.ndx and chose #1 for Protein. Many thanks for any help! Regards, Jennifer On Wed, Jan 14, 2015 at 9:09 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Wed, Jan 14, 2015 at 9:00 AM, Jennifer Vo quyvio...@gmail.com wrote: Dear All, I have got this error while running trjconv from .xtc to .pdb file. The System includes 8 Protein (4622 Atoms each, x8 = 36976 Atoms). 135978 is the total number of Atoms in the System. The index.ndx was created from md.gro file, and I Chose #1 for Protein. I don't know where is the original error of the mismatch here Fatal error: Index[4622] 135978 is larger than the number of atoms in the trajectory file (36976). There is a mismatch in the contents of your -f, -s and/or -n files. I would appreciate for any help. Providing your actual command lines and interactive choices would help. If you'd done the right things, you'd probably not be having a problem, so we'll need to know what things you actually did. ;-) Also, use gmx check on the .xtc and .tpr files, and less on the .ndx files to see whether these files contain the things you think they do. Mark Jennifer. -- 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] trjconv mismatch in number of atoms
Dear Experts, I am running a trjconv from xtc files to pdb file but have got this error: Fatal error: Index[4622] 135978 is larger than the number of atoms in the trajectory file (36976). There is a mismatch in the contents of your -f, -s and/or -n files. I don't know where the origin of the Problem, the index.ndx was created from md.gro file, the *.xtc (8 Proteins in a box, so I type #1 to have the index of 8 Proteins, each Protein has 4622 Atoms). The trajectory has 36976 Atoms which is 4622 * 8 and 135978 is the total number of Atoms in the System. I would really appreciate for your help. SIncerely, Jennifer -- 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] gmxcheck killed
Dear All,
My command was:
*gmxcheck_mpi -f md-1.trr -n index.ndx -s1 em-1.tpr -c md-1.gro -e
md-1.edr -m md1-gmxcheck.txt*
The output md1-gmxcheck.txt content was:
*\section{Methods}\subsection{Simulation system}A system of 70256 molecules
(1087816 atoms) was simulated.*
*\subsection{Simulation settings}A total of 0.5 ns were simulated with a
time step of 1 fs.Neighbor searching was performed every 1 steps.The PME
algorithm was used for electrostatic interactions.with a cut-off of 1 nm.A
reciprocal grid of 200 x 200 x 200 cells was used with 4th order B-spline
interpolation.A single cut-off of 1 was used for Van der Waals
interactions.*
There was a list of error
*Distance between atoms 956362 and 956363 is 0.098, should be 0.094*
before the *Reading frame 4 time4.000* was running and
ending as *killed*
It seems there are many problems here but I don't know where the begining
of error.
I really appreciate for any help.
Jennifer
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