Re: [AMBER] mm_pbsa vertex atom mismatch

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Tue, 9 Sep 2014 12:26:40 -0700

This comes from the molecular surface calculation in molsurf. I
remember seeing this type of errors reported on the list before.

Please do a google search on this error on the mailing list archive to
see how this was resolved in the past.

Ray 
--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Tue, Sep 9, 2014 at 5:36 AM, Fengxue Li <lifx916.126.com> wrote:
> Dear amber users：
> I am running MM-PBSA module with following ptraj input  file to genetare mdcrd file for snapshots.
> trajin ./md3.mdcrd
> strip :192-11805
> trajout ./md3.trj nobox time 2
>
>
> I am trying to calculate the binding free energy of my receptor - ligand complex (both are protein chains) using MM-PB(GB)SA. When I run the mm_pbsa script I eventually get the results(statistics.out etc.), however I also get this message too,
>
>  vertex atom mismatch
>        atom: 2825
> vertex atom: 2823
> my input file is mmpbsa.in ，this is
> .GENERAL
> PREFIX                1i8a
> PATH                  ./crd
> COMPLEX               1
> RECEPTOR              1
> LIGAND                1
> COMPT                 ./comp.prmtop
> RECPT                 ./pro.prmtop
> LIGPT                 ./lig.prmtop
> GC                    0
> AS                    0
> DC                    0
> MM                    1
> GB                    1
> PB                    1
> MS                    1
> NM                    0
> .PB
> PROC                  2
> REFE                  0
> INDI                  1.0
> EXDI                  80.0
> SCALE                 2
> LINIT                 1000
> PRBRAD                1.4
> ISTRNG                0.00
> RADIOPT               0
> NPOPT                 1
> CAVITY_SURFTEN        0.0072
> CAVITY_OFFSET         0.00
> #
> SURFTEN               0.0072
> SURFOFF               0.00
>
>
> .MM
> DIELC                 1.0
> .GB
> IGB                   2
> GBSA                  1
> SALTCON               0.05
> EXTDIEL               80.0
> INTDIEL               1.0
> SURFTEN               0.0072
> SURFOFF               0.0
> .MS
> PROBE                 0.0
> .PROGRAMS
> I searched the list but I could not figure out the problem. Anybody have an idea?
>
> Also I want to ask a second question,
> Before extracting the snapshots from the explicit water trajectory for this calculation, do we have to strip away the waters and ions with ptraj? (I mean we already define where the receptor and ligand starts and ends in the script) If we do not, does this effect the final results?
>
> Thanks for the help.
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Received on Tue Sep 09 2014 - 12:30:02 PDT
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