Hello,
This type of thing will be much easier in the upcoming AmberTools release.
It will include a topology file editor that gives you direct control over
the data in the topology file (and makes tasks like changing atomic
properties much easier).
For now, the document provided to you is the main description of most amber
file formats, including the topology file. Note that Amber charges are
multiplied by 18.2223 in the topology file (for run-time efficiency), so
this may be the cause if your confusion.
HTH,
Jason
On Wed, Oct 26, 2011 at 8:10 PM, Yao Yao <yao0o.ymail.com> wrote:
> Hi,
>
>
> I am kinda confused about the charge part in my prmtop file. It has five
> columns, and some of them obviously refer to O and H masses after protein
> solvation.
> I was just trying to change the charges antechamber created. Is there some
> document that explains the details of prmtop file, I cannot find any
> explicit info in amber manual.
>
> Thanks,
>
> Yao
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Oct 26 2011 - 18:30:02 PDT
