AMBER Archive (2007)

Subject: AMBER: Group input for restrained atoms

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Fri Nov 30 2007 - 10:28:50 CST

How to select resSeq?

The system is a protein-ligand in POPC lipid membrane, where each POPC molecule
is TIP3P hydrated at the polar head. The protein has also a water molecule of
crystallization, defined as TIP3P.

Removed lipid and water residues overlapping the protein (except the water
molecule inside the protein).

Combined the whole with "combine" in leap.

Now, where to read the "resSeq" for restraining the protein-ligand only in the
initial minimization?

Assuming that the pdb files for membrane and protein-ligand have no more
meaning, if I create from the combined top/crd the pdb file with ambpdb, first
are listed the lipid residues 1-76, then the protein residues, 77-520, then the
ligand 521, then WAT residues 522-9999 and 0-4759.

I am absolutely not sure that these are the relevant resSeq. However,I have no
idea if they can be obtained from the prmtop file and how.

I was unable to get light from tutorial and mailing list. Thanks for indicating
the procedure.

francesco pietra

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