[AMBER] TMD setup

From: Manish Datt <manishdatt.gmail.com>
Date: Mon, 6 Aug 2012 14:16:14 +0530

Hi All,

I am trying to study conformational transition in a protein using TMD
with amber10. I have prepared the two systems (reference and target)
in explicit solvent in leap using the command:
solvateOct unit TIP3PBOX 10
Although the number of atoms in protein in the two systems are same
but the total number of atoms are different because of different
conformations of the protein and hence different number of water
molecules in the box. While running the MD I specified target under
the -ref flag. This gives an error
FATAL: NATOM mismatch in constraint coord and topology files
Could you please suggest how can I prepare the two system with equal
number of atoms so that same topology file can be used for both
Thanks in advance,


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Received on Mon Aug 06 2012 - 02:00:02 PDT
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