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.
 
Thomas

--- 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

$AMBERHOME/test/cnstph

adrian

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
>> residues.
>>
>> Adrian
>>
>>
>> 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
>>
>> _______________________________________________
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>>
>
>
> 

-- 
                            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

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