[AMBER] Problem with closest command in cpptraj

From: Indrajit Deb <biky2004indra.gmail.com>
Date: Wed, 11 May 2016 16:16:14 +0200

Dear Amber users,

I am using the following 'closest' command in cpptraj (AMBER14+TOOLS15) to
write the new trajectory with one water molecule close to the geometric
center between the atoms given in the mask.

closest 1 :5.HN1,O2P oxygen center closestout closestout-seq-f-mod-idrp.dat
outprefix closest

The following cpptraj output is showing that it considering the geometric
center between the selected atoms in the mask, but I want to consider the
oxygen atom of the water molecule to calculate the distance from the
geometric center. For that, I used the 'oxygen' key. But the output showing
that only first atom of the solvent molecule was used for distance

    CLOSEST: Finding closest 1 solvent molecules to atoms in mask :5.HN1,O2P
Geometric center of atoms in mask will be used.
Only first atom of solvent molecule used for distance calc.

Please explain what wrong I am doing.

indrajit ​

*Indrajit Deb*
alternate emails: indrajitdeb81.gmail.com, idbmbg_s.caluniv.ac.in
*Present Position*
International Centre for Genetic Engineering and Biotechnology (ICGEB,
Italy) SMART Fellow,
Department of Structural Chemistry and Biology of Nucleic Acids,
Institute of Bioorganic Chemistry (IBCh),
Polish Academy of Sciences (PAS).
European Center for Bioinformatics and Genomics (ECBiG) Campus (
oom: 2.6.28
Z. Noskowskiego Str. 12/14.
Poznan 61-704, Poland​.
Phone: +48616653042, ​Personal Mobile: +48662513522​

*Previous Position*​
Ph.D Student,
Department of Biophysics, Molecular Biology and Bioinformatics, University
of Calcutta (CU), 92 APC Road, Kolkata - 700009, India. Phone:
+913323508386 (extn. 329, 321), Fax: +913323519755. Personal Mobile:
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Received on Wed May 11 2016 - 07:30:06 PDT
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