AMBER Archive (2005)

Subject: Re: AMBER: Cluster - input files

From: Ananda Rama Krishnan Selvaraj (ananda.selvaraj_at_chemie.uni-halle.de)
Date: Mon Nov 28 2005 - 14:39:44 CST

Dear Mr. David A. Case,
                         I am sorry for the confusion. yes, i tried to
make a MD simulation using Periodic Boundary Condition. In AMBER5 as
well as AMBER7 in both case i have used the same pdb file to make prmcrd
files. But the outfile from the (AMBER7) LEaP (prmcrd)has more volume
than in AMBER5.

I don't know exactly which could be the reason for the error. so that i
have mentioned the LEaP commands,

Thanks
Anand

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
Date: Monday, November 28, 2005 7:47 pm
Subject: Re: AMBER: Cluster - input files

> On Mon, Nov 28, 2005, Ananda Rama Krishnan Selvaraj wrote:
> >
> > To prepare the cluster input file in AMBER7, i have used the
> following> commands in Xleap,
> >
> > (1) first way
> >
> > 1. xleap
> > 2. source leaprc.gaff
> > 3. loadAmberPrep prep.in file name of monomer
> > 4. edit res name
> > 5. saveoff res name res name.lib
> > 6. loadoff res name.lib
> > 7. frcmod = loadamberparams frcmod
> > 8. x = loadpdb pdb-file name of the cluster
> > 9. saveAmberParm x prmtop prmcrd
> > 10. quit
> >
> > (2) second way
> >
> > 1. xleap
> > 2. source leaprc.gaff
> > 3. mods = loadamberparams frcmod
> > 4. loadAmberPrep prep.in file name of the monomer
> > 5. resseq = { resname, ........n-resname } ( n-number of monomers)
> > 6. x = loadPdbUsingSeq pdb file name of the cluster resseq
> > 7. saveAmberParm x prmtop prmcrd
> > 8. quit
> >
> > In both ways, in the co-ordinate files the volume of the box is
> same by
> > AMBER7.
> > But the co-ordinate files from AMBER5 has lower volume than in
> AMBER7.
> I am confused: neither of your examples sets up a periodic
> simulation, as far
> as I can see. What exactly do you mean by the "volume of the box"
> beingdifferent? In both of your examples, the coordinates in the
> prmcrd file
> should just be whatever was in the pdb file that you loaded: LEaP
> is not doing
> anything with these coordinates.
>
> ...dac
>
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