Re: [gmx-users] methylated HSP
Ok attachment was not a good idea, atomtypes are in this mail. [ HIC ] [ atoms ] N NH1 -0.47 0 HN H 0.311 CA CT1 0.072 HA HB1 0.093 CB CT2 -0.05 4 HB1 HA2 0.095 HB2 HA2 0.096 CD2 CPH10.197 HD2 HR1 0.138 CG CPH10.199 NE2 NR3-0.51 10 CR CT3 0.1711 HR1 HA3 0.0912 HR2 HA3 0.0913 HR3 HA3 0.0914 ND1 NR3 -0.51 15 HD1 H 0.4416 CE1 CPH20.3217 HE1 HR2 0.1818 C C 0.5119 O O -0.51 20 From: Emma Ahlstrand Sent: Tuesday, July 04, 2017 7:32 PM To: gmx-us...@gromacs.org Subject: methylated HSP Hi, I am going to simulate a protein with a methylated histidine in Gromacs using CHARMM36 FF. I name the modified aminoacid HIC, the structure is attached in pdf file. I have followed the discussion in https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat=15364=all but I cannot see that NR3 is the proper atomtype. I have tried to add bonds, angles and dihedrals for NR3 and the methyl,: [ bondtypes ] ; ij func b0 kb NR3 CT3 1 0.149 167360.00 ; inserted for methylated HIS (HIC) [ angletypes ] ; ijk func theta0 ktheta ub0 kub NR3 CT3 HA3 5 107.50 472.792000 0. 0.00 ;inserted for HIC [ dihedraltypes ] ; ijkl func phi0 kphi mult NR3 CPH2 NR3 CT3 9 180.0012.552000 2 ; inserted for HIC HR2 CPH2 NR3 CT3 9 180.0012.552000 2 ; inserted for HIC HR1 CPH1 NR3 CT3 9 0.0008.368000 2 ; inserted for HIC CPH1 CPH1 NR3 CT3 9 180.0050.208000 2 ; inserted for HIC CT1 CT2 CPH1 NR3 9 0.0 0.00 1 ; inserted for HIC CPH1 NR3 CT3 HA3 9 0.0 0.00 1 ; inserted for HIC CPH2 NR3 CT3 HA3 9 0.00 0.00 1 ; inserted for HIC [ dihedraltypes ] ; 'improper' dihedrals ; ijkl func phi0 kphi NR3 CPH1 CPH2 CT3 2 0. 10.041600 ; inserted for HIC NR3 CPH2 CPH1 CT3 2 0.0 10.041600 ; inserted for HIC CT2 CPH1 NR3 CPH1 2 0.0 0.0 ; inserted for HIC CT2 NR3 CPH1 CPH1 2 0.0 0.0 ; inserted for HIC CPH1 CPH1 NR3 HR1 2 0.0 0.0 ; inserted for HIC CPH1 NR3 CPH1 HR1 2 0.0 0.0 ; inserted for HIC CPH2 NR3 NR3 HR2 2 0.0 0.0 ; inserted for HIC but ended up with "No default U-B types" for CPH1 NR3 CT3 and CPH2 NR3 CT3 Anyone who is interested to help me find the problem? Or is there a better atomtype for the nitrogen in the HIS/imidazole ring where a methyl group can be attached. I tried NG321, but then I ran into troubles when attaching to CPH1 and CPH2. Best regards, Emma --- Emma Ahlstrand PhD student Linnaeus University Faculty of Health and Life Sciences 391 82 Kalmar / 351 95 Växjö Sweden +46 772 28 80 00 Telephone exchange +46 480 44 61 52 Direct +46 739 05 71 86 Mobile emma.ahlstr...@lnu.se http://lnu.se/ccbg Lnu.se Challenging educations. Prominent research. Linnaeus University – a modern, international university in Småland, Sweden. -- 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] methylated HSP
pdf attached now. --- Emma Ahlstrand PhD student Linnaeus University Faculty of Health and Life Sciences 391 82 Kalmar / 351 95 Växjö Sweden +46 772 28 80 00 Telephone exchange +46 480 44 61 52 Direct +46 739 05 71 86 Mobile emma.ahlstr...@lnu.se http://lnu.se/ccbg Lnu.se Challenging educations. Prominent research. Linnaeus University – a modern, international university in Småland, Sweden. From: Emma Ahlstrand Sent: Tuesday, July 04, 2017 7:32 PM To: gmx-us...@gromacs.org Subject: methylated HSP Hi, I am going to simulate a protein with a methylated histidine in Gromacs using CHARMM36 FF. I name the modified aminoacid HIC, the structure is attached in pdf file. I have followed the discussion in https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat=15364=all but I cannot see that NR3 is the proper atomtype. I have tried to add bonds, angles and dihedrals for NR3 and the methyl,: [ bondtypes ] ; ij func b0 kb NR3 CT3 1 0.149 167360.00 ; inserted for methylated HIS (HIC) [ angletypes ] ; ijk func theta0 ktheta ub0 kub NR3 CT3 HA3 5 107.50 472.792000 0. 0.00 ;inserted for HIC [ dihedraltypes ] ; ijkl func phi0 kphi mult NR3 CPH2 NR3 CT3 9 180.0012.552000 2 ; inserted for HIC HR2 CPH2 NR3 CT3 9 180.0012.552000 2 ; inserted for HIC HR1 CPH1 NR3 CT3 9 0.0008.368000 2 ; inserted for HIC CPH1 CPH1 NR3 CT3 9 180.0050.208000 2 ; inserted for HIC CT1 CT2 CPH1 NR3 9 0.0 0.00 1 ; inserted for HIC CPH1 NR3 CT3 HA3 9 0.0 0.00 1 ; inserted for HIC CPH2 NR3 CT3 HA3 9 0.00 0.00 1 ; inserted for HIC [ dihedraltypes ] ; 'improper' dihedrals ; ijkl func phi0 kphi NR3 CPH1 CPH2 CT3 2 0. 10.041600 ; inserted for HIC NR3 CPH2 CPH1 CT3 2 0.0 10.041600 ; inserted for HIC CT2 CPH1 NR3 CPH1 2 0.0 0.0 ; inserted for HIC CT2 NR3 CPH1 CPH1 2 0.0 0.0 ; inserted for HIC CPH1 CPH1 NR3 HR1 2 0.0 0.0 ; inserted for HIC CPH1 NR3 CPH1 HR1 2 0.0 0.0 ; inserted for HIC CPH2 NR3 NR3 HR2 2 0.0 0.0 ; inserted for HIC but ended up with "No default U-B types" for CPH1 NR3 CT3 and CPH2 NR3 CT3 Anyone who is interested to help me find the problem? Or is there a better atomtype for the nitrogen in the HIS/imidazole ring where a methyl group can be attached. I tried NG321, but then I ran into troubles when attaching to CPH1 and CPH2. Best regards, Emma --- Emma Ahlstrand PhD student Linnaeus University Faculty of Health and Life Sciences 391 82 Kalmar / 351 95 Växjö Sweden +46 772 28 80 00 Telephone exchange +46 480 44 61 52 Direct +46 739 05 71 86 Mobile emma.ahlstr...@lnu.se http://lnu.se/ccbg Lnu.se Challenging educations. Prominent research. Linnaeus University – a modern, international university in Småland, Sweden. -- 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] methylated HSP
Hi, I am going to simulate a protein with a methylated histidine in Gromacs using CHARMM36 FF. I name the modified aminoacid HIC, the structure is attached in pdf file. I have followed the discussion in https://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat=15364=all but I cannot see that NR3 is the proper atomtype. I have tried to add bonds, angles and dihedrals for NR3 and the methyl,: [ bondtypes ] ; ij func b0 kb NR3 CT3 1 0.149 167360.00 ; inserted for methylated HIS (HIC) [ angletypes ] ; ijk func theta0 ktheta ub0 kub NR3 CT3 HA3 5 107.50 472.792000 0. 0.00 ;inserted for HIC [ dihedraltypes ] ; ijkl func phi0 kphi mult NR3 CPH2 NR3 CT3 9 180.0012.552000 2 ; inserted for HIC HR2 CPH2 NR3 CT3 9 180.0012.552000 2 ; inserted for HIC HR1 CPH1 NR3 CT3 9 0.0008.368000 2 ; inserted for HIC CPH1 CPH1 NR3 CT3 9 180.0050.208000 2 ; inserted for HIC CT1 CT2 CPH1 NR3 9 0.0 0.00 1 ; inserted for HIC CPH1 NR3 CT3 HA3 9 0.0 0.00 1 ; inserted for HIC CPH2 NR3 CT3 HA3 9 0.00 0.00 1 ; inserted for HIC [ dihedraltypes ] ; 'improper' dihedrals ; ijkl func phi0 kphi NR3 CPH1 CPH2 CT3 2 0. 10.041600 ; inserted for HIC NR3 CPH2 CPH1 CT3 2 0.0 10.041600 ; inserted for HIC CT2 CPH1 NR3 CPH1 2 0.0 0.0 ; inserted for HIC CT2 NR3 CPH1 CPH1 2 0.0 0.0 ; inserted for HIC CPH1 CPH1 NR3 HR1 2 0.0 0.0 ; inserted for HIC CPH1 NR3 CPH1 HR1 2 0.0 0.0 ; inserted for HIC CPH2 NR3 NR3 HR2 2 0.0 0.0 ; inserted for HIC but ended up with "No default U-B types" for CPH1 NR3 CT3 and CPH2 NR3 CT3 Anyone who is interested to help me find the problem? Or is there a better atomtype for the nitrogen in the HIS/imidazole ring where a methyl group can be attached. I tried NG321, but then I ran into troubles when attaching to CPH1 and CPH2. Best regards, Emma --- Emma Ahlstrand PhD student Linnaeus University Faculty of Health and Life Sciences 391 82 Kalmar / 351 95 Växjö Sweden +46 772 28 80 00 Telephone exchange +46 480 44 61 52 Direct +46 739 05 71 86 Mobile emma.ahlstr...@lnu.se http://lnu.se/ccbg Lnu.se Challenging educations. Prominent research. Linnaeus University – a modern, international university in Småland, Sweden. -- 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] grompp_d and mdrun_d in gromacs 5.1.2
Hi, i wonder if there is a command for running with double precision in VERSION 5.1.2, like grompp_d in VERSION 4.6.5? Best regards, Emma --- Emma Ahlstrand PhD student Linnaeus University Faculty of Health and Life Sciences 391 82 Kalmar / 351 95 Växjö Sweden +46 772 28 80 00 Telephone exchange +46 480 44 61 52 Direct +46 739 05 71 86 Mobile emma.ahlstr...@lnu.se http://lnu.se/ccbg Lnu.se Challenging educations. Prominent research. Linnaeus University – a modern, international university in Småland, Sweden. -- 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] Forcefield parameters for Zinc
Hi, Related to the Zn-parameters; where can I find the reference (author, journal, year) to the sigma and epsilon (1.95998e-01 5.23000e-02) parameters that I find in /gromacs/top/amber99sb.ff/ffnonbonded.itp for [ atomtypes ] Zn. I would like to use amber99sb force field in my Gromacs simulation of a Zn- containing protein. Best regards, Emma + Join us for an exciting international meeting in Kalmar - http://ccbglinnaeus.wix.com/swedtheorchem2015 --- Emma Ahlstrand PhD student Linnaeus University Faculty of Health and Life Sciences 391 82 Kalmar / 351 95 Växjö Sweden +46 772 28 80 00 Telephone exchange +46 480 44 61 52 Direct +46 739 05 71 86 Mobile emma.ahlstrand at lnu.se http://lnu.se/ccbg Lnu.se Challenging educations. Prominent research. Linnaeus University – a modern, international university in Småland, Sweden. -- 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-request at gromacs.org. Leandro Bortot leandro.obt@... writes: Hi Emma, Just sharing some experience here: I tried to use the AMBER99SB-ILDN forcefield, which has the same Zn parameter as AMBER99SB, for simulating a Zn-binding protein and it was actually not possible to study the Zn- binding process. This happens essentially because it is not a good approximation to consider Zn2+ as a charged sphere and expect it to bind strongly to CysH, or even Cys-, and to His during the simulations because these are not simple charge-charge interactions. Some approaches for better results are to use a tetrahedral model for zinc (Cationic Dummy Atom Approach), use His-Zn and Cys-Zn bonding parameters or to perform QM/MM. I don't know about the tetrahedral model, but using bonding parameters will certainly ensure the bonded state. I believe you can find such parameters for AMBER99SB in the literature. I hope it helps, Leandro. Hi Leandro, thanks for your reply. I did not expect the parameters for Zn in Amber99sb to work directly (I was thinking of adding distance restraints on Zn-His interaction). However in a short equilibration the parameters did work and the Zn stayed in the protein as it should. So I would like to know more about the work behind these LJ sigma and epsilon parameters and how the were chosen and evaluated. Does anyone know where I find the reference to the LJ sigma and epsilon parameters that I find in /gromacs/top/amber99sb.ff/ffnonbonded.itp for [atomtypes ] Zn? Best regards, Emma -- 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] Forcefield parameters for Zinc
Piggot T. T.Piggot@... writes: Hi Mike, As well as the link that Bipin sent, you can also get parameters for GROMOS phosphorylated residues (compatible with the 43A1 force field, I think) from: http://www.gromacs.org/Downloads/User_contributions/Force_fields I've never used either so have no idea which might be better. The ones that Binpin suggested look like they work with the newer GROMOS 54A7 force field, so they might be the ones to use. On your other question, I am not sure about the protein-zinc parameters with a GROMOS force field. I would say, is there any particular need for using one of the GROMOS protein force fields? There are definitely parameters out there for some of the all-atom protein force fields (e.g. AMBER ones) which are probably also better in terms of protein parameters. Cheers Tom PS: Hope things are good in the (relatively) new job! From: gromacs.org_gmx-users-bounces@... [gromacs.org_gmx-users-bounces@...] on behalf of Michael Carter [Michael.Carter@...] Sent: 20 August 2014 12:56 To: gmx-users@... Subject: Re: [gmx-users] Forcefield parameters for Zinc and phosphorylated residues Hi Bipin, Thanks for this. It works well for adding functionality to residues. Cheers, Mike Carter On 20/08/2014 12:10, bipin singh bipinelmat@... wrote: This might help. http://vienna-ptm.univie.ac.at/ *Thanks and Regards,Bipin Singh* On Wed, Aug 20, 2014 at 4:30 PM, Michael Carter Michael.Carter@... wrote: Hi, I have two questions regarding the parameterisation of Zinc ions and a phosphorylated TYR residue within two different protein systems. 1. Zinc parameters: I have three zinc ions within one protein system. I want to use a bonded model so that they do not fly out of my protein upon simulation. Is there any documentation on the parameters for such a model in the GROMOS forcefield? 2. Phosphorylated TYR In another system I have a phosphorylated TYR residue. PDB2GMX does not like this and after looking inot the manual I have found that you can add parameters for this to the existing forcefields. Much like the previous question, is there any documentation on the addition of parameters for phosphorylated residues in the GROMOS forcefield? Any pointers for these questions would be greatly appreciated. Cheers, Mike Carter The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- 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-request@... -- 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-request@... The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- 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-request@... Hi, Related to the Zn-parameters; where can I find the reference (author, journal, year) to the sigma and epsilon (1.95998e-01 5.23000e-02) parameters that I find in /gromacs/top/amber99sb.ff/ffnonbonded.itp for [ atomtypes ] Zn. I would like to use amber99sb force field in my Gromacs simulation of a Zn- containing protein. Best regards, Emma + Join us for an exciting international meeting in Kalmar - http://ccbglinnaeus.wix.com
[gmx-users] Changed order of molecules in top
Hi, I have a problem with that the order of atoms in my topology does not match the order of atoms in the gro-file. I use amber99sb and I have built itp-files on my own for the molecules that are not present in the library. Each IMI contains 9 atoms and each SOL 3 atoms and the ZN is one atom so in total it should be 9*2+3*2+1=25 atoms in total, which is present in the .gro file, but when I run with the topology-file pasted below I get a error the this file contains 34 atoms. This is my topologyfile: ; Include forcefield parameters #include amber99sb.ff/forcefield.itp ; Additional atom types [ atomtypes ] ; name at_name at_num mass charge ptype sigmaepsilon ; sw ref Zn++ Zn++30 65.37000 2.000A1.94216e-01 1.046 ; 1 Stote Proteins 23:12 1995 ; Include topology for ions #include zn.itp ; Include water topology #include spcetestamber.itp ; Include topology for imidazole #include imiamberrtp.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif [system ] ; Name ZnHis2Wa2 [ molecules ] ; Compound#mols ZN2+ 1 IMI 2 SOL 2 - Fatal error: number of coordinates in coordinate file (ZnHis2Wa2optM06.gro, 25) does not match topology (ZnHis2Wa2optM06amber.top, 34) Since the difference is 9 atoms, I thought that the difference is one IMI, so I tried with one less IMI in the topology, printed below. ; Include forcefield parameters #include amber99sb.ff/forcefield.itp ; Additional atom types [ atomtypes ] ; name at_name at_num mass charge ptype sigmaepsilon ; sw ref Zn++ Zn++30 65.37000 2.000A1.94216e-01 1.046 ; 1 Stote Proteins 23:12 1995 ; Include topology for ions #include zn.itp ; Include water topology #include spcetestamber.itp ; Include topology for imidazole #include imiamberrtp.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif [system ] ; Name ZnHis2Wa2 [ molecules ] ; Compound#mols ZN2+ 1 IMI 1 SOL 2 Then the number of atoms matches, but I get the information that the atom names does not match. Warning: atom name 1 in ZnHis2Wa2optM06ambertest.top and ZnHis2Wa2optM06.gro does not match (C1 - ZN) Warning: atom name 2 in ZnHis2Wa2optM06ambertest.top and ZnHis2Wa2optM06.gro does not match (N1 - C1) By this message it gets clear to me that the topology makes an IMI first and then go on to the ZN and then probably the IMI and the two waters specified in the top-file. Why does it do that? And how do I correct it? Thanks in advance for help. -- Emma Ahlstrand PhD student Linnaeus University Faculty of Health and Life Sciences 391 82 Kalmar / 351 95 Växjö +46 480 446 152 Telephone +46 73 905 7186 Mobile emma.ahlstr...@lnu.se http://lnu.se/ccbg -- 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] Changed order of molecules in top
Justin Lemkul jalemkul@... writes: On 7/2/14, 3:31 AM, Emma Ahlstrand wrote: Hi, I have a problem with that the order of atoms in my topology does not match the order of atoms in the gro-file. I use amber99sb and I have built itp-files on my own for the molecules that are not present in the library. Each IMI contains 9 atoms and each SOL 3 atoms and the ZN is one atom so in total it should be 9*2+3*2+1=25 atoms in total, which is present in the .gro file, but when I run with the topology-file pasted below I get a error the this file contains 34 atoms. This is my topologyfile: ; Include forcefield parameters #include amber99sb.ff/forcefield.itp ; Additional atom types [ atomtypes ] ; name at_name at_num mass charge ptype sigmaepsilon ; sw ref Zn++ Zn++30 65.37000 2.000A1.94216e-01 1.046 ; 1Stote Proteins 23:12 1995 ; Include topology for ions #include zn.itp ; Include water topology #include spcetestamber.itp ; Include topology for imidazole #include imiamberrtp.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif [system ] ; Name ZnHis2Wa2 [ molecules ] ; Compound#mols ZN2+ 1 IMI 2 SOL 2 - Fatal error: number of coordinates in coordinate file (ZnHis2Wa2optM06.gro, 25) does not match topology (ZnHis2Wa2optM06amber.top, 34) Since the difference is 9 atoms, I thought that the difference is one IMI, so I tried with one less IMI in the topology, printed below. ; Include forcefield parameters #include amber99sb.ff/forcefield.itp ; Additional atom types [ atomtypes ] ; name at_name at_num mass charge ptype sigmaepsilon ; sw ref Zn++ Zn++30 65.37000 2.000A1.94216e-01 1.046 ; 1Stote Proteins 23:12 1995 ; Include topology for ions #include zn.itp ; Include water topology #include spcetestamber.itp ; Include topology for imidazole #include imiamberrtp.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif [system ] ; Name ZnHis2Wa2 [ molecules ] ; Compound#mols ZN2+ 1 IMI 1 SOL 2 Then the number of atoms matches, but I get the information that the atom names does not match. Warning: atom name 1 in ZnHis2Wa2optM06ambertest.top and ZnHis2Wa2optM06.gro does not match (C1 - ZN) Warning: atom name 2 in ZnHis2Wa2optM06ambertest.top and ZnHis2Wa2optM06.gro does not match (N1 - C1) By this message it gets clear to me that the topology makes an IMI first and then go on to the ZN and then probably the IMI and the two waters specified in the top-file. Why does it do that? And how do I correct it? No, your coordinate file has IMI first. grompp expects the input coordinates and topology to be in the same order. You list Zn, IMI, and SOL in the .top - that is the expected order in the coordinates. As reported by grompp, that is not the case. There should be no probably here; with such a small system it should be very easy to inspect the .gro file in a text editor and see precisely what is going on. -Justin Hi Justin, the problem is that my coordinate file (ZnHis2Wa2optM06.gro) has Zn first and then two IMI and then two water and this is what I think I make with my topology file as well, but the topology seems to produce an IMI first? ZnHis2Wa2 25 1Zn++ZN1 1.495 1.497 1.361 2MOL C12 1.293 1.499 1.588 2MOL N13 1.324 1.561 1.451 2MOL C24 1.166 1.556 1.632 ... Regards, Emma -- 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] Changed order of molecules in top
Without seeing the full contents of all the files, none of this really makes sense. If you can provide a link to download the full (1) topology and all related .itp files, (2) coordinates, and (3) .mdp files, I will take a look. -Justin Hi again, thanks a lot for taking your time. Here is a link to the top (and test.top with just one IMI), the gro, the itp´s, and the mdp files. https://www.dropbox.com/s/dmz41drsjr0bqkn/ZnHis2Wa2.tar.gz I hope this kind of link works. Best regards, Emma -- 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] Distance restraints does not work?
Thanks Justin. I was concerned about that the distance could increase so much above 0.4 (I had the feeling from the equation that the penalty was larger above up2(0.4)). 50.0000.4642269 100.0000.4505744 But anyway when I checked the interactions to Zn I found a competing interaction with an oxygen that could play a role. When I got rid of that and decreased up2 to 0.3 I got what I wanted. /Emma -- View this message in context: http://gromacs.5086.x6.nabble.com/Distance-restraints-does-not-work-tp5013284p5013341.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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.
