AMBER Archive (2006)

Subject: AMBER: mm_pbsa snapshots for "three-trajectory"

From: In Hee Park (ipark_at_chemistry.ohio-state.edu)
Date: Thu Sep 14 2006 - 18:42:13 CDT

Amber community,

Could you let me know the way to extract snapshot for
"three-trajectory(3T)" using mm_pbsa.in? Especially how can I define the
trajectory file name in @TRAJECTORY section for complex, ligand, and
receptor at once there?

So far I have been prepared the trajectories for 3T one by one for
complex, ligand and receptor each time only using RECEPTOR-related parameters,
(and then convert the resulting snapshots' file name from **_rec.crd.## to
**_com.crd.## or **_lig.crd.##), noting that the following note in the mm_pbsa.in.
####
# Note: If only one molecular species is extracted, use only the receptor
# parameters (NUMBER_REC_GROUPS, RSTART, RSTOP).
####

Thanks in advance.

___________________
In Hee Park
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