Hi Arturas,
You can try sander using imin=5 (that's how mm_pbsa perl script does)
or, an easier way is to use VMD, loading your prmtop and trajectory
and selecting the atoms (or residues) you want in the NAMDEnergy
plugin window.
I recently compared the VDW / Elec energy as computed by VMD and
mm_pbsa and they were in perfect agreement. So, should be ok....
HTH,
--alessandro
On Thu, Aug 14, 2008 at 9:21 AM, Arturas Ziemys
<arturas.ziemys.uth.tmc.edu> wrote:
> Hi,
>
> I can not find approach in Amber to calculate non-bonded interactions for a
> chosen pair of atom groups. Any search leads just to MM-PBSA... Could anyone
> give some idea ?
>
> Best,
> Arturas
>
>
>
>
> --
>
> Arturas Ziemys, PhD
> School of Health Information Sciences
> University of Texas Health Science Center at Houston
> 7000 Fannin, Suit 880
> Houston, TX 77030
> Phone: (713) 500-3975
> Fax: (713) 500-3929
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--
[ ]s
--alessandro
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Received on Sun Aug 17 2008 - 06:07:46 PDT
