AMBER Archive (2009)

Subject: [AMBER] How to build reference coordinate file for targeted MD

From: gmail (heptoking_at_gmail.com)
Date: Thu Feb 05 2009 - 00:44:22 CST

Dear All
    I am trying to do a targeted MD for a big protein. There is a question on how to build a reference
coordinate file. As the manual pointed out that the reference coordinate are expected to match the prmtop
file of the starting structure. However, the starting and final structures are two different pdb files,
which although have the same amino acid sequence, the exact atom sequence are somewhat different. In addition,
 I am thinking that if I create the solvated reference prmtop and inpcrd files, the number of water molecules
will be slightly different to those generated with starting pdb file. That will most probably cause failure of
recognition.


With no definite solution in my mind, I have to ask experts for suggestions.


Thank you in advance.


Cheers!


Xiaonan Zhang

Shanghai public health clinical center

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