Ben Cossins wrote:
>Hi Dave and Ray,
> Thanks for the replies. I have added "fillratio=4" to the pbsa input
>creation script. I still seem to be getting the same problems. Not sure
>why. If anyone has any other ideas then please help.
>
>Thanks
>
>Ben
>
>
Hi Ben,
Please email me your pbsa input file, parm file, and the snapshots that
you see the smallest and the largest solvation free energies. I'll be
happy to take a look.
Ray
>
>On Wednesday 15 Dec 2004 06:17, Ray Luo wrote:
>
>
>>Ben Cossins wrote:
>>
>>
>>>Hi Dave and Ray,
>>> Sorry for the delayed reply and thanks for your help. I am still having
>>>trouble. My ligands are not so small they are all over 85 atoms. I have
>>>increased the fillratio (by this a take it you mean the number of grid
>>>points/area) again and am still getting fluctuating solvation energies.
>>>
>>>
>>Ben,
>>
>>fillratio is not grid points/area. This is a new keyword added to the
>>pbsa program. See Amber webpage.
>>
>>Best,
>>Ray
>>
>>
>>
>>>However they seem to fluctuate less as I increase the SCALE parameter.
>>>With 6 grid points per angstrom it fluctates from about -2600 to -50
>>>while the surface area values stay stable around 980. I am unable to
>>>work through the pbsa code and find what the problem is. Can you give me
>>>an idea of what i could try.
>>>
>>>sorry to bother you again
>>>
>>>Ben
>>>
>>>
>
>
>
--
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528 Lab: (949)824-9562
Fax: (949)824-8551 e-mail: rluo.uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
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Received on Wed Dec 15 2004 - 17:53:00 PST
