[AMBER] distance mapping

From: <monica.imtech.res.in>
Date: Fri, 30 Apr 2010 20:21:48 +0530 (IST)

hi all

1. can anyone suggest any way by which the long axis diameter can be calculated
for the different snapshots of a protein molecule whose MD was run for different
time intervals.

2. is there any way of calculating number of water molecules or change in
solvation (or hydration) status during MD only for the active site.

3. how to calculate the volume of an active site in general or for different md

4. can anyone provide any information of basic outline how to set up a QM/MM
dynamics. any tutorial or link will b appreciated.

5. finally how can i access to maximum possible use of ptraj modules. any link
where it has been listed out.

thanx a lot in advance

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Received on Fri Apr 30 2010 - 08:00:07 PDT
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