[gmx-users] mdrun outputs incorrect resnames
tsjerkw at gmail.com
Sun May 26 08:12:44 CEST 2013
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.
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.
> On Sun, May 26, 2013 at 12:31 AM, Reid Van Lehn <rvanlehn at gmail.com>
> > 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
> > 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
> > 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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