[gmx-users] Re: pair interaction energy decomposition analysis

you could check your .ndx file and make sure the atoms 389 and 391 are listed under the same group (i.e. protein ROU) Alternately, you could try using energygrps= System Please make sure that the value for energygrps is one of the groups listed in the .ndx file Shounak -- View this message in con

[gmx-users] Re: pdb2gmx error

Hi, C and O should be atoms 14 and 15 (i.e. the last two atoms) Hope this works! Shima Arasteh wrote > >  Hi all, > > I got this error : > Atom CA is used in an interaction of type improper in the topology > database, but an atom of that name was not found in residue number 2. > I checked the

[gmx-users] Re: pdb2gmx error

Hi, C and O should go last (i.e. their atom numbers should be 14 and 15 respectively. Hope this works! Regards, Shounak Shima Arasteh wrote > >  Hi all, > > I got this error : > Atom CA is used in an interaction of type improper in the topology > database, but an atom of that name was not fo

[gmx-users] Re: pdb2gmx error

gt;> The order of atoms in the .pdb file is irrelevant.  What may be the issue >> is >> that when pdb2gmx is reporting the error, it is printing its own internal >> residue number (i.e., the second residue in the chain) - are you missing >> residue >> 1?  Files downloa

[gmx-users] Re: pdb2gmx error

Shima, I use gromacs-4.5.4. Without the FOR residue, my gmx.ff/aminoacids.rtp file works fine for the sequence you originally specified. (pdb2gmx executes without any errors) I guess you added the FOR cap's topology yourself? Justin, could this be an issue? Sincerely, Shounak -- View this messag

[gmx-users] Re: pdb2gmx error

erely, > Shima > > > - Original Message - > From: Justin A. Lemkul <jalemkul@> > To: Discussion list for GROMACS users <gmx-users@> > Cc: > Sent: Wednesday, June 27, 2012 10:25 PM > Subject: Re: [gmx-users] Re: pdb2gmx error > > > >

[gmx-users] Re: pdb2gmx error

sorry about the previous post! I have not yet looked at the code for pdb2gmx (and a lot of other stuff). I think the formyl-valine idea is pretty cool and found this thread very informative. Thank you! Shounak Justin A. Lemkul wrote > > On 6/27/12 2:49 PM, shounakb wrote: >> Hi Shim

[gmx-users] Re: Re:Shell scripts

Hi, you might want to try the following code in bash #!/bin/bash i=1 while [ $i -le 1322 ] do g_energy -f traj_$i.edr -o $i.xvg << EOF i=`expr $i + 1` done Hope this helps! Shounak lloyd riggs wrote > > Dear All, > > So I am using some scripts to parse through 100s of files using bash a

[gmx-users] Re: Re:Shell scripts

Hi, you might want to try the following code in bash. I do not know if you specifically need to create a "here-document" #!/bin/bash i=1 while [ $i -le 1322 ] do g_energy -f traj_$i.edr -o $i.xvg i=`expr $i + 1` done Hope this helps! Shounak lloyd riggs wrote > > Dear All, > > So I am usi