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

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

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

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

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

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 ( >

[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

Re: [gmx-users] Residue XXX not found in residue topology database

On 8/26/19 8:27 PM, Neena Susan Eappen wrote: Hello gromacs users, I saw the following error for a modified residue I added though I edited all necessary files including PDB. I also read the gromacs documentation on this error. Residue XXX not found in residue topology database. Any

[gmx-users] Residue XXX not found in residue topology database

Hello gromacs users, I saw the following error for a modified residue I added though I edited all necessary files including PDB. I also read the gromacs documentation on this error. Residue XXX not found in residue topology database. Any hints on what might be happening? Many thanks, Neena