[gmx-users] mdrun outputs incorrect resnames

[Reid Van Lehn]

Great, thank you that did the trick. My fault for not realizing this
earlier.

Best,
Reid


On Sun, May 26, 2013 at 2:12 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> No, the residue names are the those from the .top file. But that's not the
> same as the moleculetypes. You have to change the residue names in the [
> atoms ] section.
>
> Cheers,
>
> Tsjerk
>
>
> On Sun, May 26, 2013 at 12:57 AM, Mark Abraham <mark.j.abraham at gmail.com
> >wrote:
>
> > AFAIK, the residue names in the mdrun output .gro file are those of the
> > structure file you gave to grompp.
> >
> > Mark
> >
> >
> > On Sun, May 26, 2013 at 12:31 AM, Reid Van Lehn <rvanlehn at gmail.com>
> > wrote:
> >
> > > Hello,
> > >
> > > I am simulating a lipid bilayer and wish to apply position restraints
> to
> > > only a subset of the lipids in the bilayer. Since position restraints
> are
> > > applied to all molecules of the same molecule type, I defined a new
> > > molecule type (DOPR) which is identical to my lipid species (DOPC) by
> > > copying the lipid itp file, renaming it and renaming the corresponding
> > > molecule type. I then manually edited a starting .gro file to change a
> > > subset of the DOPC molecules to DOPR, edited my topology,
> > > renumbered/reordered, etc. I also recreated the index file to account
> for
> > > the new molecules so that temperature coupling could be used correctly.
> > >
> > > Everything seemed ok when I ran the mdrun - grompp didn't complain, the
> > > program ran normally, the output trajectory clearly used the correct
> > > position restraints, etc. The weird part, though, is that the output
> .gro
> > > file at the end of the simulation only had DOPC molecules in it - the
> > DOPR
> > > molecules that I had renamed by hand had somehow been output as DOPC
> > > instead. Positions, number of atoms, everything else was fine, just the
> > > name of the residues was different. I can't figure out why this is
> > > happening. It was reproducible across both GMX 4.5.5 / 4.6 and multiple
> > > different starting files.
> > >
> > > It's not a huge issue since the trajectories themselves are fine, I'm
> > just
> > > worried this issue might indicate other, less obvious problems. A
> snippet
> > > of the topol file is below if that is helpful.
> > >
> > > Any suggestions / advice would be appreciated!
> > >
> > > ********************************
> > > #include "forcefield.itp
> > > #include "dopc.itp"
> > >
> > > #ifdef POSRES
> > > #include "dopc-posre.itp"
> > > #endif
> > >
> > > ; Always include DOPR restraints for restrained lipids
> > > #include "dopc_restrained.itp"
> > > #include "dopr-posre.itp"
> > >
> > > #include "spc.itp"
> > > #include "ions.itp"
> > >
> > > [ system ]
> > > ; Name
> > > frame t= 1.000 in water
> > >
> > > [ molecules ]
> > > ; Compound        #mols
> > > DOPC             398
> > > DOPR               2
> > > SOL            63882
> > > NA               179
> > > CL               179
> > > *********************************
> > >
> > > Thanks,
> > > Reid
> > > --
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
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-- 
Reid Van Lehn
NSF/MIT Presidential Fellow
Alfredo Alexander-Katz Research Group
Ph.D Candidate - Materials Science