Hi Xiaodu, Yes I remember now I had the same problem. Copy the forcefield.itp to your working directory and make the change there. Your working directory is searched first. However as you will be including a protein in your simulation you will need to have fudge set to 0.5 for 1-4 scaling with the AMBER forcefield... Personally I would look into doing mixed scaling with gromacs. This is how it is done in amber (the software package) when mixing these two forcefields but I can't help you here with gromacs, but I believe from reading the AMBER mailing list archive it is possible to scale on a per molecule basis.
http://dev-archive.ambermd.org/200812/0000.html Here is the relevant part of the thread: Hi Rob, It was great to see you yesterday at the glycan array workshop. I'm here with Erik Lindahl, and we're chatting about implementing mixed 1-4 scaling in gromacs. It's easy to enable on a per-molecule basis. Enabling on a per-residue and per-atom basis is certainly possible, but there are a bunch of ways to do it. Do you have a sense of how you'd like to see this done? One idea would be to enable two different 1-4 pair types, one with default 1-4 scaling and one with user-specified scaling. And how should the interface be handled? I assume that it goes to default at that point (we want the protein 1-4 scaling at the NLN). Best wishes, --Peter 2010/12/27 gromacs564 <gromacs...@126.com> > Hi Oliver > > I'm sorry to reply you so later.And I have some questions after reading your > letter. > > You said that “The fudgeLJ under defaults should be 1.0 for GLYCAM“ and ”When > you run grompp check in the > > output that fudge is set to 1.0.” Do you means to setting the fudgeLJ value > to 1.0 in em.tpr file？I am not sure. > > I want to change this gromacs top files( all the output files by amb2gmx.pl > converted) to gromacs itp files,then included in protein top file. And I plan > to use the amber03 force filed. But I think that the "[ defaults ]" cannot > included in itp files,or will cause an error about redifiniton.Because the "[ > defaults ]" had exist in ”forcefield.itp". > > ------------------------------------------------------------------------------------------ > > ;myt.itp > > [ defaults ] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 1 2 yes 0.5（ =1.0 ? ） 0.8333 > > ------------------------------------------------------------------------------------------------ > > #define _FF_AMBER > #define _FF_AMBER03 > > [ defaults ] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 1 2 yes 0.5 0.8333 > > ---------------------------------------------------------------------------------------------------------- > > So，do you know how to slove this problem？Can you give me some suggestion > or a correct copy file by > > amb2gmx.pl converted? Thank you very much. > > My email address：gromacs...@126.com > > xiaodu > > > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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