AMBER Archive (2008)

Subject: AMBER: Setting GROUP for pmemd

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Oct 30 2008 - 14:10:39 CDT


The pdb is
RES 1 78 lipid POPC

RES 79 340 protein with capping groups (included in numbering)

RES 341 ligand
====

Input for pmemd to restrain protein ligand and POPC (the other residues are WAT)

/
Keep ...
32.0
RES 1 341
END
EnD

worked fine.
=========

The I moved to sander.MPI in order to be able to restrain protein,
ligand and a part only of lipid. Now back to pmemd to restrain protein
and ligand only

/
Keep ..
32.0
RES 79 341
END
END

the out file:
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM AND COORDINATES
READING GROUP 1;TITLE:
GROUP 1 HAS HARMONIC CONSTRAINTS 32.00000
GRP 1 RES 79 TO 341
number of atoms ...
READING GROUP 2; TITLE:
END
GROUP 2 HAS HARMONIC CONSTRAINTS 0.00000
rfree: End of file on unit 5
====================

Thanks a lot for pointing out my mistake.

francesco pietra
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