AMBER Archive (2007)

Subject: Re: AMBER: Group input for restrained atoms

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Fri Nov 30 2007 - 15:12:42 CST

There is no macroscopic overlapping. That water with same resID as the protein
is relegated into two regions in the shell outside the membrane. I found that
rather extraordinary because there are no chainIDs (column 22 does not exist)
nor CONECTs. That from editing in order that leap could accept pdbs written by
other software.

My understanding of your kind answer is that resID can be derived from the pdb
amdpdb-built from top/crd.

What will happen during the const volume minimization is difficult to foresee,
however, as there is some overlapping in the POPC region. My feeling was that
the plugin has problems in building large membranes.

Thanks
francesco

--- Pavan G <pavanamber_at_gmail.com> wrote:

> 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
> anyway,
> ----------
> Minimization with Cartesian restraints
> &cntrl
> 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).
>
> Cheers
> Pavan
>
> On Nov 30, 2007 11:28 AM, Francesco Pietra <chiendarret_at_yahoo.com> 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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