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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Received on Fri Oct 31 2008 - 05:11:40 PDT
