Hi Oliver,
Keep in mind that the receptor_mask and ligand_mask correspond to the masks
within the complex, NOT within the solvated_prmtop. Thus, you should always
be able to use the default mask guesser in your case (see below)
On Thu, Apr 21, 2011 at 7:24 AM, Oliver Kuhn <oak.amber.googlemail.com>wrote:
> Hi there,
>
> The resulting numbering is
> 1-198 protein
> 199 ligand
> 200-204 chloride ions
> 205 water to be included in the MMPBSA calculation
> 206 ... many waters
>
> So I'm trying
> receptor_mask=:1-198
> ligand_mask=:199:205
> but of course I can't use the old com.top rec.top and lig.top because the
> water is not in there.
>
receptor_mask is correct, but there will be no chloride ions in the stripped
complex, so the ligand mask should be :199-200, which is something the
default guesser can handle just fine, so I would suggest that you omit
these.
>
> So I'm trying to build new ones as follows:
> source leaprc.ff03
> source leaprc.gaff
> loadAmberParams ../apv.frcmod
> rec=loadpdb ../rec.pdb
> lig=loadmol2 ../apv.mol2
> wat=loadpdb ../wat.pdb
>
> lig=combine{lig wat}
>
> com=combine{rec lig}
>
> saveamberparm rec rec.top rec.crd
> savepdb rec rec.pdb
> saveamberparm lig lig.top lig.crd
> savepdb lig lig.pdb
> saveamberparm com com.top com.crd
> savepdb com com.pdb
>
> If I now use these com.top rec.top and lig.top I get an error:
>
> Preparing trajectories with ptraj...
> 1000 frames were read in and processed by ptraj for use in calculation.
>
> Starting calculations...
>
> Starting pb calculation...
>
> calculating ligand contribution...
> Unable to allocate memory!
> (This often means you don't have enough memory available for this
> calculation.)
> VASSERT: ASSERTION FAILURE! filename vmem.c, line 249, (ram != ((void
> *)0))
> sh: line 1: 30482 Abgebrochen
> /usr/local/amber11/bin/sander.APBS
> -O -i _MMPBSA_pb.mdin -o _MMPBSA_ligand_pb.mdout -p lig.top -c
> _MMPBSA_dummyligand.inpcrd -y _MMPBSA_ligand.mdcrd -r _MMPBSA_.restrt >>
> _MMPBSA_pbsanderoutput.junk
> calculating receptor contribution...
>
> .... and so on ......
>
>
> So, I have the impression that I do not really grep the water - and do not
> know what happens there .
>
> The _MMPBSA_cenptraj.in file reads as follows:
> trajin ../prod.10ps_steps.mdcrd 1 1000 1
> strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
>
>
Right here it shows that you didn't change strip_mask. This mask will strip
out ALL waters, even the one you want to keep. If you are positive that the
one water you want to keep is #205, then set strip_mask in your input file
to ":200-204,205-END" (whatever your end residue is). However, it's quite
likely that waters will exchange, and you'll want to post-process the
trajectory yourself (i.e. with 'closest') in order to keep the correct
water.
HTH,
Jason
How can I get the right com.top rec.top lig.top fitting to my simulation
> data to do my calculation?
>
>
> Thanks for any answers,
> regards,
> Oliver
>
>
> Oliver Kuhn, Department of Bioinformatics,
> Center for Medical Biotechnology, University of Duisburg-Essen,
> Universitätsstr. 1-5, 45141 Essen, Germany
> phone +49 201 183-3121, oliver.kuhn.uni-due.de
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Apr 21 2011 - 08:30:02 PDT
