Re: [gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files

I could understand if it was doing this within pdb2gmx or something that was constructing a topology file. I'm observing this behavior when using editconf to simply convert files to another format or apply box dimensions etc. Anyway, I submitted a bugzilla about it. This isn't such a big problem -

Re: [gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files

On 6/14/2007 1:14 AM, Erik Lindahl wrote: Hi Robert, On Jun 13, 2007, at 6:48 PM, Robert Johnson wrote: These are all fine points. However, the question I'm asking is why do Gromacs tools change atoms named OXT in PDB files to O2? Of course there are always workarounds i.e. just simply change

Re: [gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files

Robert Johnson wrote: These are all fine points. However, the question I'm asking is why do Gromacs tools change atoms named OXT in PDB files to O2? Of course there are always workarounds i.e. just simply change the atom name in the coordinate file. However, I was wondering if anyone knew why thi

Re: [gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files

Hi Robert, On Jun 13, 2007, at 6:48 PM, Robert Johnson wrote: These are all fine points. However, the question I'm asking is why do Gromacs tools change atoms named OXT in PDB files to O2? Of course there are always workarounds i.e. just simply change the atom name in the coordinate file. Howev

Re: [gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files

These are all fine points. However, the question I'm asking is why do Gromacs tools change atoms named OXT in PDB files to O2? Of course there are always workarounds i.e. just simply change the atom name in the coordinate file. However, I was wondering if anyone knew why this happened. I suppose I

Re: [gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files

Hi, I think that the terminal oxygen atoms should not be named OXT for the amber forcefields but rather OC1 and OC2. To check this look in the top folder at the ffamberXX.rtp file. Hope this helps Tom --On Tuesday, June 12, 2007 15:30 -0400 Robert Johnson <[EMAIL PROTECTED]> wrote: Hell

Re: [gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files

Robert Johnson wrote: Hello everyone, I'm attempting to run a simulation of a protein that contains an atom named OXT (for the terminal oxygen atom). We are using the amber force field and have already successfully built a topology for the protein. However, when running Grompp we consistently rec

[gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files

Hello everyone, I'm attempting to run a simulation of a protein that contains an atom named OXT (for the terminal oxygen atom). We are using the amber force field and have already successfully built a topology for the protein. However, when running Grompp we consistently receive the following erro