[AMBER] Problem regarding Same coordinate for two atoms

From: Hirdesh Kumar <hirdesh.iitd.gmail.com>
Date: Sat, 22 Jan 2011 12:04:37 +0530

Hi Amber Users,
I am trying to heat my protein ligand complex at constant volume. But it is
showing SHAKE error. I googled the error and found that it is due to overlap
of the coordinate. I tested the same using ptraj close contact utility. I
generated the .pdb file from the .parm7 and .rst file and change the
coordinate of overlapping hydrogen. But Now I am stuck how to convert my
protein (*.pdb format*) back into the .parm7 and .crd file. One option is by
using tleap again on my complex, but for that I need the parameter file for
my solvent molecule (i.e. TIP3P). Is there any other option for the same??

Thanks and Regard,
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Received on Fri Jan 21 2011 - 23:00:04 PST
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