Re: [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6
It was a typos. In the .pdb file I wrote SnC as residue name, while in .rtp file it was still written SnCl. That's why the error. Thanks a lot again. Paolo Il dom 19 apr 2020, 22:05 Justin Lemkul ha scritto: > > > On 4/19/20 3:47 PM, Paolo Costa wrote: > > Hi Justin, > > > > I could fix the issue. > > > > Thanks again for your help. > > And in the spirit of helping others that use this mailing list, what > exactly was the problem and how did you solve it? > > -Justin > > > Paolo > > > > Il giorno dom 19 apr 2020 alle ore 21:35 Justin Lemkul > ha > > scritto: > > > >> > >> On 4/17/20 5:25 PM, Paolo Costa wrote: > >>> Hi Justin, > >>> > >>> thanks a lot. I tried as you said and I changed from SnCl6 to SnC in my > >>> stannate.pdb and also to stannate.rtp. But still I get the error. > >>> Here the output file of from pdb2gmx: > >>> > >>> Opening force field file > /usr/share/gromacs/top/amber99.ff/aminoacids.r2b > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/dna.r2b > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/rna.r2b > >>> Reading stannate.pdb... > >>> WARNING: all CONECT records are ignored > >>> Read 'stannate', 7 atoms > >>> Analyzing pdb file > >>> Splitting chemical chains based on TER records or chain id changing. > >>> There are 1 chains and 0 blocks of water and 1 residues with 7 atoms > >>> > >>> chain #res #atoms > >>> 1 ' ' 1 7 > >>> > >>> All occupancy fields zero. This is probably not an X-Ray structure > >>> Opening force field file > /usr/share/gromacs/top/amber99.ff/atomtypes.atp > >>> Atomtype 68 > >>> Reading residue database... (amber99) > >>> Opening force field file > /usr/share/gromacs/top/amber99.ff/aminoacids.rtp > >>> Residue 93 > >>> Sorting it all out... > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/benzene.rtp > >>> Residue 94 > >>> Sorting it all out... > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/dna.rtp > >>> Residue 110 > >>> Sorting it all out... > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/rna.rtp > >>> Residue 126 > >>> Sorting it all out... > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/stannate.rtp > >>> Residue 127 > >>> Sorting it all out... > >>> Opening force field file > /usr/share/gromacs/top/amber99.ff/aminoacids.hdb > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/dna.hdb > >>> Opening force field file /usr/share/gromacs/top/amber99.ff/rna.hdb > >>> Opening force field file > >> /usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb > >>> Opening force field file > >> /usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb > >>> Back Off! I just backed up topol.top to ./#topol.top.19# > >>> Processing chain 1 (7 atoms, 1 residues) > >>> > >>> Warning: Starting residue SnC0 in chain not identified as > >> Protein/RNA/DNA. > >>> This chain lacks identifiers, which makes it impossible to do strict > >>> classification of the start/end residues. Here we need to guess this > >> residue > >>> should not be part of the chain and instead introduce a break, but that > >> will > >>> be catastrophic if they should in fact be linked. Please check your > >>> structure, > >>> and add SnC to residuetypes.dat if this was not correct. > >>> > >>> Problem with chain definition, or missing terminal residues. > >>> This chain does not appear to contain a recognized chain molecule. > >>> If this is incorrect, you can edit residuetypes.dat to modify the > >> behavior. > >>> 8 out of 8 lines of specbond.dat converted successfully > >>> > >>> --- > >>> Program: gmx pdb2gmx, version 2018.1 > >>> Source file: src/gromacs/gmxpreprocess/resall.cpp (line 639) > >>> > >>> Fatal error: > >>> Residue 'SnC' not found in residue topology database > >>> > >>> *Thanks a lot for helping!* > >> Without seeing the contents of the PDB file and stannate.rtp, there's > >> not much to go on here. > >> > >> -Justin > >> > >> -- > >> == > >> > >> Justin A. Lemkul, Ph.D. > >> Assistant Professor > >> Office: 301 Fralin Hall > >> Lab: 303 Engel Hall > >> > >> Virginia Tech Department of Biochemistry > >> 340 West Campus Dr. > >> Blacksburg, VA 24061 > >> > >> jalem...@vt.edu | (540) 231-3129 > >> http://www.thelemkullab.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. > >> > > > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > >
Re: [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6
On 4/19/20 3:47 PM, Paolo Costa wrote: Hi Justin, I could fix the issue. Thanks again for your help. And in the spirit of helping others that use this mailing list, what exactly was the problem and how did you solve it? -Justin Paolo Il giorno dom 19 apr 2020 alle ore 21:35 Justin Lemkul ha scritto: On 4/17/20 5:25 PM, Paolo Costa wrote: Hi Justin, thanks a lot. I tried as you said and I changed from SnCl6 to SnC in my stannate.pdb and also to stannate.rtp. But still I get the error. Here the output file of from pdb2gmx: Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.r2b Opening force field file /usr/share/gromacs/top/amber99.ff/dna.r2b Opening force field file /usr/share/gromacs/top/amber99.ff/rna.r2b Reading stannate.pdb... WARNING: all CONECT records are ignored Read 'stannate', 7 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 1 residues with 7 atoms chain #res #atoms 1 ' ' 1 7 All occupancy fields zero. This is probably not an X-Ray structure Opening force field file /usr/share/gromacs/top/amber99.ff/atomtypes.atp Atomtype 68 Reading residue database... (amber99) Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.rtp Residue 93 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/benzene.rtp Residue 94 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/dna.rtp Residue 110 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/rna.rtp Residue 126 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/stannate.rtp Residue 127 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.hdb Opening force field file /usr/share/gromacs/top/amber99.ff/dna.hdb Opening force field file /usr/share/gromacs/top/amber99.ff/rna.hdb Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.19# Processing chain 1 (7 atoms, 1 residues) Warning: Starting residue SnC0 in chain not identified as Protein/RNA/DNA. This chain lacks identifiers, which makes it impossible to do strict classification of the start/end residues. Here we need to guess this residue should not be part of the chain and instead introduce a break, but that will be catastrophic if they should in fact be linked. Please check your structure, and add SnC to residuetypes.dat if this was not correct. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program: gmx pdb2gmx, version 2018.1 Source file: src/gromacs/gmxpreprocess/resall.cpp (line 639) Fatal error: Residue 'SnC' not found in residue topology database *Thanks a lot for helping!* Without seeing the contents of the PDB file and stannate.rtp, there's not much to go on here. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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. -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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.
Re: [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6
Hi Justin, I could fix the issue. Thanks again for your help. Paolo Il giorno dom 19 apr 2020 alle ore 21:35 Justin Lemkul ha scritto: > > > On 4/17/20 5:25 PM, Paolo Costa wrote: > > Hi Justin, > > > > thanks a lot. I tried as you said and I changed from SnCl6 to SnC in my > > stannate.pdb and also to stannate.rtp. But still I get the error. > > Here the output file of from pdb2gmx: > > > > Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.r2b > > Opening force field file /usr/share/gromacs/top/amber99.ff/dna.r2b > > Opening force field file /usr/share/gromacs/top/amber99.ff/rna.r2b > > Reading stannate.pdb... > > WARNING: all CONECT records are ignored > > Read 'stannate', 7 atoms > > Analyzing pdb file > > Splitting chemical chains based on TER records or chain id changing. > > There are 1 chains and 0 blocks of water and 1 residues with 7 atoms > > > >chain #res #atoms > >1 ' ' 1 7 > > > > All occupancy fields zero. This is probably not an X-Ray structure > > Opening force field file /usr/share/gromacs/top/amber99.ff/atomtypes.atp > > Atomtype 68 > > Reading residue database... (amber99) > > Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.rtp > > Residue 93 > > Sorting it all out... > > Opening force field file /usr/share/gromacs/top/amber99.ff/benzene.rtp > > Residue 94 > > Sorting it all out... > > Opening force field file /usr/share/gromacs/top/amber99.ff/dna.rtp > > Residue 110 > > Sorting it all out... > > Opening force field file /usr/share/gromacs/top/amber99.ff/rna.rtp > > Residue 126 > > Sorting it all out... > > Opening force field file /usr/share/gromacs/top/amber99.ff/stannate.rtp > > Residue 127 > > Sorting it all out... > > Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.hdb > > Opening force field file /usr/share/gromacs/top/amber99.ff/dna.hdb > > Opening force field file /usr/share/gromacs/top/amber99.ff/rna.hdb > > Opening force field file > /usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb > > Opening force field file > /usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb > > > > Back Off! I just backed up topol.top to ./#topol.top.19# > > Processing chain 1 (7 atoms, 1 residues) > > > > Warning: Starting residue SnC0 in chain not identified as > Protein/RNA/DNA. > > This chain lacks identifiers, which makes it impossible to do strict > > classification of the start/end residues. Here we need to guess this > residue > > should not be part of the chain and instead introduce a break, but that > will > > be catastrophic if they should in fact be linked. Please check your > > structure, > > and add SnC to residuetypes.dat if this was not correct. > > > > Problem with chain definition, or missing terminal residues. > > This chain does not appear to contain a recognized chain molecule. > > If this is incorrect, you can edit residuetypes.dat to modify the > behavior. > > 8 out of 8 lines of specbond.dat converted successfully > > > > --- > > Program: gmx pdb2gmx, version 2018.1 > > Source file: src/gromacs/gmxpreprocess/resall.cpp (line 639) > > > > Fatal error: > > Residue 'SnC' not found in residue topology database > > > > *Thanks a lot for helping!* > > Without seeing the contents of the PDB file and stannate.rtp, there's > not much to go on here. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.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. > -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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] Residue ‘XXX’ not found in residue topology database - SnCl6
On 4/17/20 5:25 PM, Paolo Costa wrote: Hi Justin, thanks a lot. I tried as you said and I changed from SnCl6 to SnC in my stannate.pdb and also to stannate.rtp. But still I get the error. Here the output file of from pdb2gmx: Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.r2b Opening force field file /usr/share/gromacs/top/amber99.ff/dna.r2b Opening force field file /usr/share/gromacs/top/amber99.ff/rna.r2b Reading stannate.pdb... WARNING: all CONECT records are ignored Read 'stannate', 7 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 1 residues with 7 atoms chain #res #atoms 1 ' ' 1 7 All occupancy fields zero. This is probably not an X-Ray structure Opening force field file /usr/share/gromacs/top/amber99.ff/atomtypes.atp Atomtype 68 Reading residue database... (amber99) Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.rtp Residue 93 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/benzene.rtp Residue 94 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/dna.rtp Residue 110 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/rna.rtp Residue 126 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/stannate.rtp Residue 127 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.hdb Opening force field file /usr/share/gromacs/top/amber99.ff/dna.hdb Opening force field file /usr/share/gromacs/top/amber99.ff/rna.hdb Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.19# Processing chain 1 (7 atoms, 1 residues) Warning: Starting residue SnC0 in chain not identified as Protein/RNA/DNA. This chain lacks identifiers, which makes it impossible to do strict classification of the start/end residues. Here we need to guess this residue should not be part of the chain and instead introduce a break, but that will be catastrophic if they should in fact be linked. Please check your structure, and add SnC to residuetypes.dat if this was not correct. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program: gmx pdb2gmx, version 2018.1 Source file: src/gromacs/gmxpreprocess/resall.cpp (line 639) Fatal error: Residue 'SnC' not found in residue topology database *Thanks a lot for helping!* Without seeing the contents of the PDB file and stannate.rtp, there's not much to go on here. -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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.
Re: [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6
Hi Justin, thanks a lot. I tried as you said and I changed from SnCl6 to SnC in my stannate.pdb and also to stannate.rtp. But still I get the error. Here the output file of from pdb2gmx: Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.r2b Opening force field file /usr/share/gromacs/top/amber99.ff/dna.r2b Opening force field file /usr/share/gromacs/top/amber99.ff/rna.r2b Reading stannate.pdb... WARNING: all CONECT records are ignored Read 'stannate', 7 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 1 residues with 7 atoms chain #res #atoms 1 ' ' 1 7 All occupancy fields zero. This is probably not an X-Ray structure Opening force field file /usr/share/gromacs/top/amber99.ff/atomtypes.atp Atomtype 68 Reading residue database... (amber99) Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.rtp Residue 93 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/benzene.rtp Residue 94 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/dna.rtp Residue 110 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/rna.rtp Residue 126 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/stannate.rtp Residue 127 Sorting it all out... Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.hdb Opening force field file /usr/share/gromacs/top/amber99.ff/dna.hdb Opening force field file /usr/share/gromacs/top/amber99.ff/rna.hdb Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.n.tdb Opening force field file /usr/share/gromacs/top/amber99.ff/aminoacids.c.tdb Back Off! I just backed up topol.top to ./#topol.top.19# Processing chain 1 (7 atoms, 1 residues) Warning: Starting residue SnC0 in chain not identified as Protein/RNA/DNA. This chain lacks identifiers, which makes it impossible to do strict classification of the start/end residues. Here we need to guess this residue should not be part of the chain and instead introduce a break, but that will be catastrophic if they should in fact be linked. Please check your structure, and add SnC to residuetypes.dat if this was not correct. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully --- Program: gmx pdb2gmx, version 2018.1 Source file: src/gromacs/gmxpreprocess/resall.cpp (line 639) Fatal error: Residue 'SnC' not found in residue topology database *Thanks a lot for helping!* Paolo Il giorno ven 17 apr 2020 alle ore 22:55 Justin Lemkul ha scritto: > On Fri, Apr 17, 2020 at 4:50 PM Paolo Costa > wrote: > > > Dear GROMACS user, > > > > I am aware that such error occurs frequently for new users as I am. > > I am learning how to add new residue in Gromacs; I tried first following > a > > tutorial ( > > https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-water/ ) > > and later by creating a benzene, C6H6 molecule, using amber99.ff force > > field. Everything goes fine without any problems. > > > > For the next step I tried to create residue for a molecule, SnCl6, for > > which there are no parameters (just for training). Thus, within > amber99.ff, > > I add in the atomtypes.atp the atom Sn with the corresponding mass (the > Cl > > (chlorine) was already present). Then, I add in ffnonbonded.itp the LJ > > parameters for Sn (again for Cl there are already present). Finally I add > > in ffbonded.itp the parameters for bond stretch and angle (I calculated > > them by Gaussian and VFFDT software). > > > > I created *my .pdb file* as following: > > COMPNDstannate > > REMARK1 File created by GaussView 6.0.16 > > HETATM1 Sn SnCl6 0 0.000 0.000 0.000 > > Sn > > HETATM2 Cl1 SnCl6 0 -0.000 0.000 2.502 > > Cl > > HETATM3 Cl2 SnCl6 0 -0.000 2.502 -0.000 > > Cl > > HETATM4 Cl3 SnCl6 0 2.502 0.000 0.000 > > Cl > > HETATM5 Cl4 SnCl6 0 -0.000 -2.502 0.000 > > Cl > > HETATM6 Cl5 SnCl6 0 -2.502 0.000 -0.000 > > Cl > > HETATM7 Cl6 SnCl6 0 -0.000 -0.000 -2.502 > > Cl > > END > > CONECT12345 > > CONECT167 > > CONECT21 > > CONECT31 > > CONECT41 > > CONECT51 > > CONECT61 > > CONECT71 > > > > > > and *the .rtp file* which I add in the amber99.ff folder: > > [ SnCl6 ] > > [ atoms ] > > SnSn1.2468 1 > > Cl1 Cl -0.5411 2 > > Cl2 Cl -0.5411 3 > > Cl3 Cl -0.5411 4 > > Cl4 Cl -0.5411 5 > > Cl5 Cl -0.5411 6 > > Cl6 Cl -0.5411 7 > > [ bonds ] > > Sn Cl1 > > Sn Cl2 > > Sn Cl3 > > Sn Cl4 > > Sn Cl5 > > Sn Cl6 >
Re: [gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6
On Fri, Apr 17, 2020 at 4:50 PM Paolo Costa wrote: > Dear GROMACS user, > > I am aware that such error occurs frequently for new users as I am. > I am learning how to add new residue in Gromacs; I tried first following a > tutorial ( > https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-water/ ) > and later by creating a benzene, C6H6 molecule, using amber99.ff force > field. Everything goes fine without any problems. > > For the next step I tried to create residue for a molecule, SnCl6, for > which there are no parameters (just for training). Thus, within amber99.ff, > I add in the atomtypes.atp the atom Sn with the corresponding mass (the Cl > (chlorine) was already present). Then, I add in ffnonbonded.itp the LJ > parameters for Sn (again for Cl there are already present). Finally I add > in ffbonded.itp the parameters for bond stretch and angle (I calculated > them by Gaussian and VFFDT software). > > I created *my .pdb file* as following: > COMPNDstannate > REMARK1 File created by GaussView 6.0.16 > HETATM1 Sn SnCl6 0 0.000 0.000 0.000 > Sn > HETATM2 Cl1 SnCl6 0 -0.000 0.000 2.502 > Cl > HETATM3 Cl2 SnCl6 0 -0.000 2.502 -0.000 > Cl > HETATM4 Cl3 SnCl6 0 2.502 0.000 0.000 > Cl > HETATM5 Cl4 SnCl6 0 -0.000 -2.502 0.000 > Cl > HETATM6 Cl5 SnCl6 0 -2.502 0.000 -0.000 > Cl > HETATM7 Cl6 SnCl6 0 -0.000 -0.000 -2.502 > Cl > END > CONECT12345 > CONECT167 > CONECT21 > CONECT31 > CONECT41 > CONECT51 > CONECT61 > CONECT71 > > > and *the .rtp file* which I add in the amber99.ff folder: > [ SnCl6 ] > [ atoms ] > SnSn1.2468 1 > Cl1 Cl -0.5411 2 > Cl2 Cl -0.5411 3 > Cl3 Cl -0.5411 4 > Cl4 Cl -0.5411 5 > Cl5 Cl -0.5411 6 > Cl6 Cl -0.5411 7 > [ bonds ] > Sn Cl1 > Sn Cl2 > Sn Cl3 > Sn Cl4 > Sn Cl5 > Sn Cl6 > > However, although to my eyes I did everything OK, I get such error. > *Please, can somebody help me to figure out where I am doing wrong? * > PDB format only allows 4 characters in a residue name. Rename to something else (in the correct columns of the fixed format) and if that doesn’t fix it, please provide the full screen output from pdb2gmx. -Justin > Thanks a lot in advance. > > Paolo Costa > > -- > Paolo Costa, Ph.D. > Postdoctoral Researcher > Department of Chemistry and Biomolecular Sciences > University of Ottawa > 10 Marie Curie, Ottawa, ON K1N 6N5, Canada > Room number: DRO 326 (D'Iorio Hall) > -- > 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. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.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.
[gmx-users] Residue ‘XXX’ not found in residue topology database - SnCl6
Dear GROMACS user, I am aware that such error occurs frequently for new users as I am. I am learning how to add new residue in Gromacs; I tried first following a tutorial (https://www.svedruziclab.com/tutorials/gromacs/2-methane-in-water/ ) and later by creating a benzene, C6H6 molecule, using amber99.ff force field. Everything goes fine without any problems. For the next step I tried to create residue for a molecule, SnCl6, for which there are no parameters (just for training). Thus, within amber99.ff, I add in the atomtypes.atp the atom Sn with the corresponding mass (the Cl (chlorine) was already present). Then, I add in ffnonbonded.itp the LJ parameters for Sn (again for Cl there are already present). Finally I add in ffbonded.itp the parameters for bond stretch and angle (I calculated them by Gaussian and VFFDT software). I created *my .pdb file* as following: COMPNDstannate REMARK1 File created by GaussView 6.0.16 HETATM1 Sn SnCl6 0 0.000 0.000 0.000 Sn HETATM2 Cl1 SnCl6 0 -0.000 0.000 2.502 Cl HETATM3 Cl2 SnCl6 0 -0.000 2.502 -0.000 Cl HETATM4 Cl3 SnCl6 0 2.502 0.000 0.000 Cl HETATM5 Cl4 SnCl6 0 -0.000 -2.502 0.000 Cl HETATM6 Cl5 SnCl6 0 -2.502 0.000 -0.000 Cl HETATM7 Cl6 SnCl6 0 -0.000 -0.000 -2.502 Cl END CONECT12345 CONECT167 CONECT21 CONECT31 CONECT41 CONECT51 CONECT61 CONECT71 and *the .rtp file* which I add in the amber99.ff folder: [ SnCl6 ] [ atoms ] SnSn1.2468 1 Cl1 Cl -0.5411 2 Cl2 Cl -0.5411 3 Cl3 Cl -0.5411 4 Cl4 Cl -0.5411 5 Cl5 Cl -0.5411 6 Cl6 Cl -0.5411 7 [ bonds ] Sn Cl1 Sn Cl2 Sn Cl3 Sn Cl4 Sn Cl5 Sn Cl6 However, although to my eyes I did everything OK, I get such error. *Please, can somebody help me to figure out where I am doing wrong? * Thanks a lot in advance. Paolo Costa -- Paolo Costa, Ph.D. Postdoctoral Researcher Department of Chemistry and Biomolecular Sciences University of Ottawa 10 Marie Curie, Ottawa, ON K1N 6N5, Canada Room number: DRO 326 (D'Iorio Hall) -- 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.
