[gmx-users] Problem implementing REST

[Mark Abraham]

Hi,

What GROMACS version is this? What bits of your topology are being
complained about?

Mark

On Thu, Oct 16, 2014 at 11:12 AM, carlo martinotti <
specialkender at hotmail.com> wrote:

> I'm currently trying to implement Replica Exchange with Solute Tempering
> in gromacs, as previously done by terakawa et al (On easy implementation of
> a variant of the replica exchange with solute tempering in GROMACS, J
> Comput Chem. 2011 May;32(7):1228-34. doi: 10.1002/jcc.21703. Epub 2010 Nov
> 29.)
> From what i understood you have to change ffnonbonded.itp adding new
> atomtypes with perturbed LJ parameters, then change ffbonded.itp adding new
> bond/angles and dihedral types between this perturbed atoms with modifed
> harmonic constant, and that's it for the forcefield.
> Then you have to prepare a topology with state A and state B with state B
> having perturbed charges and the atom types corresponding to the perturbed
> version of the state A atoms.
> Now, i have some problems. I'm trying to modify amber03 forcefield, but
> when i try to run grompp it gives me this errors:
>
> ERROR 1 [file topol.top, line 199]:  Cannot automatically perturb a
> torsion with multiple terms to different  form.  Please specify perturbed
> parameters manually for this torsion in your  topology!
> ERROR 2 [file topol.top, line 202]:  Cannot automatically perturb a
> torsion with multiple terms to different  form.  Please specify perturbed
> parameters manually for this torsion in your  topology!
>
> ERROR 3 [file topol.top, line 205]:  Cannot automatically perturb a
> torsion with multiple terms to different  form.  Please specify perturbed
> parameters manually for this torsion in your  topology!
>
> ERROR 4 [file topol.top, line 206]:  Cannot automatically perturb a
> torsion with multiple terms to different  form.  Please specify perturbed
> parameters manually for this torsion in your  topology!
> Now, it seems that gromacs can't do this operation with amber, but in the
> article that i read they actually used amber03, so what should i do? This
> are my files mdp top ffbonded ffnonbonded
> Can somebody explain me where is the problem?
> --
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