Hi, I presume the position-restraints file was written by a tool that didn't anticipate this use case (and pdb2gmx likely does not). If so, I would edit my position restraints file to express my intent, ie copy the functype and parameters so that there's an A and B state on the same line, just as with other topology pieces.
One could also use grompp -maxwarn, but laziness leads to hate, and hate leads to the Dark Side. You will one day curse Past Hermann, because a warning you ignored costs you months of wasted simulation time. Mark On Wed, Aug 9, 2017 at 11:27 AM Hermann, Johannes < [email protected]> wrote: > Dear all, > > I have a questions concerning MD free energy calculations using > alchemical tranformation. I want to restrain the backbone of my protein > which I mutate during TI. However, I do not know how to correctly > generate position restrains. If I use the position restrain file, which > I generated for the A state, following warning shows up: > > WARNING 1 [file posre.itp, line 1470]: > Some parameters for bonded interaction involving perturbed atoms are > specified explicitly in state A, but not B - copying A to B > > Can I ignore this warning, or do you have any suggestions for me? > > All the best and thank you very much in advance > > Johannes > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to [email protected]. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
