Okay, I found the source of the problem. Like you suggested, I edited the
structure and viewed the atom types. The sugar atoms had gaff atom types. So
I just have to change them to Glycam-types and everything should work. Thank
you very much!
Josua
-----Original Message-----
From: Aron Broom [mailto:broomsday.gmail.com]
Sent: Thu 11/8/2012 5:10 PM
To: AMBER Mailing List
Subject: Re: [AMBER] different force fields for different molecules in leap
I maybe wrong, but you should source both the leaprc.gaff and leaprc.GLYCAM
when you load your combined structure (the atom types don't overlap so
everything should be fine). You can double check in LeAP by doing "edit
yourunit" and then selecting all the atoms and viewing their table and
checking on atom types. All the atom types for your sustiva should match
something found in $AMBERHOME/dat/leap/parm/gaff.dat and similarly for the
sugar.
Does sourcing the glycan forcefield also automatically source one of the
AMBER ffs? If not, how are you defining parameters for a protein? Do you
have sugars on the protein? I would have thought you'd also need to source
something like leaprc.ff12sb no?
~Aron
On Thu, Nov 8, 2012 at 11:04 AM, Pecher, Josua <
josua.pecher.stud.uni-goettingen.de> wrote:
> Hi there,
>
> I want to run a simulation with one molecule described by the GAFF force
> field and the other by GLYCAM.
>
> I followed tutorial 4b (http://ambermd.org/tutorials/basic/tutorial4b/),
> used
> the GAFF molecule where the sustiva was used and the GLYCAM molecule where
> the protein was used. I used "combine" to put the two molecules into one
> structure and everything went fine. However, just for checking, I did the
> same procedure, but only sourced the leaprc.gaff before combining the
> molecules and compared the resulting prmtop file with the former one. There
> was no difference, meaning in the first case, GAFF was used for both
> molecules.
>
> I haven't found a solution online yet, so it would be great if anybody
> could
> help me out.
>
>
> Cheers,
> Josua
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Thu Nov 08 2012 - 08:30:05 PST
