Re: AMBER: Group input for restrained atoms

From: Pavan G <>
Date: Fri, 30 Nov 2007 11:43:23 -0500

I not very sure if I understood you but here go my comments:
There is no large scale movement in the molecules during minimization unless
there are really bad overlaps. Should you feel like constraining them
Minimization with Cartesian restraints
imin=1, maxcyc=200, (invoke minimization)
ntpr=5, (print frequency)
ntr=1, (turn on Cartesian restraints)
restraint_wt=1.0, (force constant for restraint)
restraintmask=':1-58', (atoms in residues 1-58 restrained)
from the amber9 manual should work. Also you probably you dont want a water
molecule and an amino acid to have the same residue number while
constraining them (not a big deal if there are no overlaps).


On Nov 30, 2007 11:28 AM, Francesco Pietra <> wrote:

> 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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Received on Sun Dec 02 2007 - 06:07:38 PST
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