AMBER Archive (2004)

Subject: Re: AMBER: H bond calculation of CHARMM trajactory using PTRAJ

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Wed Oct 20 2004 - 09:16:50 CDT

> I am trying to use ptraj for analysis of trajactories given by CHARMM
> runs. I calculated the distance between hydrogen bond donor and acceptors

Dear Anshul, the discrepancy between the hbond/distance results processing
a PDB versus a CHARMM trajectory with ptraj is a little disconcerting.

Can you send me the PSF and DCD file so I can test this out?

\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy, Depts of
| Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry
| Adjunct Asst Prof of Bioengineering; Center for High Performance Computing
| University of Utah, 30 South 2000 East, Skaggs 201, Salt Lake City, UT 84112
|
| tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
\ BPRP295A / INSCC 418 http://www.chpc.utah.edu/~cheatham

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