[gmx-users] glycam force field problem

[Oliver Grant]

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 <gromacs564 at 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：gromacs564 at 126.com
>
> xiaodu
>
>
>
>
>
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