The easiest way to do this right now would probably be to just change the
charges in xleap or tleap and recreate the topology file that way. I would
suggest against modifying the topology file directly unless you're confident
about what you're doing. Sander and pmemd are not equipped to catch and
report on errors caused by incorrect topology file modifications, so you
could be in for a world of hurt if you do it incorrectly.
HTH,
Jason
Also, you should probably keep these responses to the whole mailing list.
On Wed, Oct 26, 2011 at 10:35 PM, Yao Yao <yao0o.ymail.com> wrote:
> Hi,
>
> Thanks for you guys' reply. So if I need to change the charges of some
> atoms in my system (say, simulate the excited state of my protein),
> could I use xleap or I have to manually modify the prmtop file, or maybe
> there exists some other way I can try?
>
> Thanks,
>
> Yao Yao
>
>
>
> ------------------------------
> *From:* Jason Swails <jason.swails.gmail.com>
> *To:* Yao Yao <yao0o.ymail.com>; AMBER Mailing List <amber.ambermd.org>
> *Sent:* Wednesday, October 26, 2011 6:21 PM
> *Subject:* Re: [AMBER] prmtop details
>
> 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
> _______________________________________________
> 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
>
>
>
--
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 - 20:00:10 PDT
