[AMBER] Problem with atommap in cpptraj

From: Rajeswari A. <rajeswari.biotech.gmail.com>
Date: Wed, 16 Jul 2014 19:34:15 +0530

Dear amber users,
I have two topology files (top1 and top2) in which the structure, charge,
coordinates, total atom number everything identical but the atom order is
different. I have trajectory that corresponds to topology1. Now i want to
reorder the trajectory based on the atom order of top2. I am using atommap
command of cpptraj in amber14.

To test the reordering i tried atommap for single pdb structure using the
following command.

parm target.top
reference target.pdb
parm complex.top
reference complex.pdb parmindex 1
atommap target.pdb complex.pdb mapout atommap.dat
trajin target.pdb
trajout reordered.pdb pdb

I expect target.pdb to reorder similar to complex.pdb. However, the
resultant reordered.pdb is not matching with the complex.pdb. Could someone
help me to sort out this? Detailed log file is attached for your reference.

Thanks in advance,
Rajeswari A.

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Received on Wed Jul 16 2014 - 07:30:03 PDT
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