VMD-L Mailing List

From: bo liu (liubo.njuer_at_gmail.com)
Date: Fri Oct 03 2008 - 06:51:22 CDT

Hi Rudra,

2008/10/3 Rudra Banerjee <bnrj.rudra_at_yahoo.com>

> I am little confused!! i think parameter file is not residue
> specific and hence if I can submit right 'type' of
> atoms in the file whose topology file is otherway running
> fine, it should work fine!!

You are right! it would work fine.

the Force Field only considers two things: 1. how atoms are connected
(topology of the simulation system). 2. atom types (so that proper
parameters can be assinged to the potential function). Once you have
correct .PSF file to describe the topology and specify atom type to all the
atoms, MD simulation will go. It is not necessary for you to follow
nomenclature conventions in describing the structure because Force Field is
atom specific but not residue specific, however, you have to follow
nomernclature conventions in describing atom types in .PSF file to
corresponding atoms. e.g. CA means the atom is assumed to be carbon atoms in
benzene, CA is the symbol that can be recognized by the force field.

>
> in my case, i have generated the topology file and solvated
> it to the water and upto that it is working fine. but given
> that i am not getting the right type of atom for tha
> non-ring N, it is giving some error at the time of MD

It seems that you have already got the right topology but you don't know
which type should some atoms be.

Regarding to the errors complained by your MD package, i guess you have
tried to assign atom types to undefined atoms but your Force Field file does
not contain relevant information to assign parameters to the potential
function. For example, if you assign an atom to be CA, you have to make sure
that all the bonds, angles, dihedrals containing this atom are also
described in the Force Field file, otherwise, the MD package cannot figure
out how to calculate, say, bond energy, angle nergy or dihedral energy in
which this atom involves.

Regarding to which atom type the undifined atoms in your structure should
be, i recommand you do some comparative study between your structure and
pre-defined structure in CHARMM ff, for example, in my opinion, the C11 in
your structure can be assumed to be type CT3 in CHARMM ff.

It would be useful for us to help you out if you can present the error
message complained by the MD package.

Cheers!

LIU BO

>
>
>
> --
> Rudra
> JRF; SNBNCBS
> http://www.bose.res.in/~rudra
>
> A bus station is where a bus stops. A train station is
> where a train
> stops. On my desk I have a work station.
>
> Please, if possible, don't send me MS Word or
> PowerPoint attachments
> Why?See:
> http://www.gnu.org/philosophy/no-word-attachments.html
>
>
> >
> > --- On Thu, 2/10/08, Axel Kohlmeyer
> > <akohlmey_at_cmm.chem.upenn.edu> wrote:
> >
> > > From: Axel Kohlmeyer
> > <akohlmey_at_cmm.chem.upenn.edu>
> > > Subject: Re: vmd-l: atom type
> > > To: "Rudra Banerjee"
> > <bnrj.rudra_at_yahoo.com>
> > > Cc: "VMD Mailing List"
> > <vmd-l_at_ks.uiuc.edu>, "John Stone"
> > <johns_at_ks.uiuc.edu>
> > > Date: Thursday, 2 October, 2008, 11:46 PM
> > > On Thu, 2 Oct 2008, Rudra Banerjee wrote:
> > >
> > > RB> no no...you misunderstood my question. I was
> > not
> > > seeking help on
> > > RB> nomenclature of atom. rather i need to specify
> > the
> > > atom type of the
> > > RB> said atoms so that there is bond given in
> > parameter
> > > file.
> > >
> > > as has been pointed out several times before.
> > >
> > > if you want to use CHARMM parameters, you have to have
> > a
> > > _proper_
> > > parameter file with the corresponding topology _and_
> > > parameters
> > > for this specific residue. that will take care of
> > bonding
> > > as well.
> > >
> > > if you don't have this - and that seems to be the
> > case
> > > - you either
> > > have to use a different force field that is supposed
> > to be
> > > more
> > > "portable" (with the risk of being less
> > accurate)
> > > or generate the
> > > missing parameters for yourself following the
> > instructions
> > > of the
> > > publications on CHARMM force field parameterization.
> > the
> > > latter
> > > is a non-trivial task except for small modifications
> > to
> > > existing
> > > topologies, and - of course - requires that you know
> > the
> > > chemistry
> > > of your compound well.
> > >
> > > cheers,
> > > axel.
> > >
> > > RB>
> > > RB>
> > > RB>
> > >
> > > --
> > >
> > =======================================================================
> > > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu
> > > http://www.cmm.upenn.edu
> > > Center for Molecular Modeling -- University of
> > > Pennsylvania
> > > Department of Chemistry, 231 S.34th Street,
> > Philadelphia,
> > > PA 19104-6323
> > > tel: 1-215-898-1582, fax: 1-215-573-6233,
> > office-tel:
> > > 1-215-898-5425
> > >
> > =======================================================================
> > > If you make something idiot-proof, the universe
> > creates a
> > > better idiot.
> >
> >
> > Add more friends to your messenger and enjoy! Go to
> > http://messenger.yahoo.com/invite/
>
>
> Add more friends to your messenger and enjoy! Go to
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>
>
> 

-- 
-Liu bo
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Computational Biochemistry&Biophysics, Nano-bio systems: MD method;
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