[gmx-users] Problem implementing REST

carlo martinotti specialkender at hotmail.com
Thu Oct 16 11:12:11 CEST 2014


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? 		 	   		  


More information about the gromacs.org_gmx-users mailing list