AMBER Archive (2009)
Subject: [AMBER] WATERSHELL
From: Mannan (malie_03_at_yahoo.co.in)
Date: Mon Aug 31 2009 - 00:02:51 CDT
Hi AMBER people,
I have used WATERSHELL in ptraj for set of trj files.
In the first frame I got 400 value for 3.5 A distance.
But when I see in VMD I could see only 5 water molecules within 3.5 for a set of residues.
How come this big difference. Do i miss anything.
Is that possible to writeout pdb with water molecules within 3.5 for a set of residues from traj.
--- On Sun, 30/8/09, Adrian Roitberg <roitberg_at_qtp.ufl.edu> wrote:
From: Adrian Roitberg <roitberg_at_qtp.ufl.edu>
Subject: Re: [AMBER] Changing pH of the system
To: "AMBER Mailing List" <amber_at_ambermd.org>
Date: Sunday, 30 August, 2009, 9:48 PM
nicholus bhattacharjee wrote:
> Dear Adrian,
> I am sorry for the mistake of writing temperature
> instead of pH. I just want to simulate my protein in different different
> pHs. Which test example should I follow? Thank you for the advice.
> On Sun, Aug 30, 2009 at 11:26 AM, Adrian Roitberg <roitberg_at_qtp.ufl.edu>wrote:
>> Dear Nicholus,
>> I am confused about your post. You say you want to simulated it at
>> different pHs and then ask how to regulate the temperature. These are two
>> different questions.
>> if you want to do constant pH, read the manual please and one of the tests
>> examples under amber. It is not trivial to set up, but perfectly doable. For
>> starters, you will need to recreate your prmtop with the protonable
>> nicholus bhattacharjee wrote:
>>> Dear community,
>>> I am trying to simulate my protein in different
>>> pH values. I am using Amber 9. Can anyone tell me how to regulate the
>>> temperature. Thank you in advance.
>> Dr. Adrian E. Roitberg
>> Associate Professor
>> Quantum Theory Project
>> Department of Chemistry
>> Senior Editor. Journal of Physical Chemistry
>> American Chemical Society
>> University of Florida PHONE 352 392-6972
>> P.O. Box 118435 FAX 352 392-8722
>> Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
>> AMBER mailing list
Dr. Adrian E. Roitberg
Quantum Theory Project
Department of Chemistry
Senior Editor. Journal of Physical Chemistry
American Chemical Society
University of Florida PHONE 352 392-6972
P.O. Box 118435 FAX 352 392-8722
Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
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