Re: Re: Creating topology for carbon nanotube / any new structure

From: prateeksha s (prateeksha.s_at_gmail.com)
Date: Fri Feb 22 2008 - 00:17:12 CST

Hi all,

Has anyone tried writing topology file entries for a new molecule?
I did not get the correct psf though i wrote entries for my molecule(cnt) in
the top. file. You see I had included only bond info in the top file(apart
from atom,mass etc) , and given auto generation for angles and dihedrals in
the psfgen prog. The angles and dihedrals were auto generated. But, while
simulating I get zero energies for dihedrals and impropers. This I am sure
is because the psf is not proper. Hence, the topology file i used to gen it
is not proper. Which implies I have to specify dihedral and improper info in
the topology file. Which I don't know how to obtain from the pdb/bgf file i
have. Have you met this hurdle? How did you deal with it?

Pls let me know anything you can.

Thanks and regards,
Prateeksha

On Sun, Jan 20, 2008 at 10:35 AM, prateeksha s <prateeksha.s_at_gmail.com>
wrote:

>
> Hello,
>
> Yes I did figure out a way to generate the *psf* file and *pdb* , from a*bgf
> * file. This works for any molecule(set). [I'm using CHARMM]
>
> I used *psfgen * to generate psf, from an existing pdb. So, I translated
> bgf to pdb using *babel* . If you are dealing with a non-standard
> molecule - simply , a molecule which does not have description in the
> topology file, you will have to write entries into the topology file -
> info on atoms, bonds and more, of the molecule.
>
> So, to start with you should know the format of *all* the files which play
> a part in your code, even if it came with some package. So, I got to know
> the format of pdb, psf, bgf, topology and parameter files. (When you get to
> know what all data you have on hand, and then what you need, you'll
> automatically get to know/search how to go about manipulating that data to
> solve your prob. ) And, generated topology info (best to delete all entries
> from the topology file and keep only your residue(s) info ).
>
> Also, if you have generated your own pdb file ( from some source ) then
> you can verify/convert it to the correct CHARMM format using the *xleap*'s
> *convpdb.pl *script.
>
> All the best,
> Prateeksha
>
> PS: It is best to go through doing the above said things yourself first,
> instead of directly using somebody's code. That's how you'll learn, so that
> you can do it easily the next time onwards.
> Also, please post on the NAMD mailing list, so that any exchange of
> ideas/solns can be available to people with similar probs.
>
> On Jan 20, 2008 6:22 AM, Dibyadeep Paul <dibyadeep_at_gmail.com> wrote:
>
> > Hii..
> >
> > I am undergraduate student from IIT Kharagpur. Actually I am trying to
> > simulate the interaction between a protein and a cnt. However I too found
> > problems in how to generate the psf file. I saw from your posts on the namd
> > mailing list that you had found a way out.
> >
> > If it is not too much of a time crunch, would it be possible for you to
> > elaborate how you did it. It would also be good if you could kindly send me
> > the psf file that you generated.
> >
> > Sincerely
> >
> > DIbyadeep
> >
>
>
> On Dec 20, 2007 9:54 AM, prateeksha s <prateeksha.s_at_gmail.com> wrote:
>
> > Hi ,
> >
> > Thanks a lot.
> >
> > I did find another way generate topology info , but from a bgf. The
> > 'CONECT' statements are nothing but BONDS and that could be used to create
> > charmm topology info . The formats are different , so you can't just copy
> > paste the CONECT against BOND in charmm top. ... The format in bgf file goes
> > like this :
> >
> > CONECT 1 2 24
> >
> > which means 1 is connected to 2 and 1 is connected to 24 .
> >
> > In charmm topology file the same thing is written as :
> >
> > BOND C1 C2 C1 C24
> >
> > rgds
> > prateeksha
> >
> >
> > On Dec 19, 2007 9:04 PM, Joseph Heil <jpheil_at_ncsu.edu> wrote:
> >
> > > there is a script in the Bionano tutorial that will give you a psf
> > > file
> > > from a pdb file, by passing the psf generator.
> > >
> > > Joseph
> > >
> > > prateeksha s wrote:
> > > > Hi all,
> > > >
> > > > I have a Carbon nanotube (6,6) pdb , and I'm trying to generate a
> > > psf
> > > > file for it . The problem is that the topology file used for
> > > > generating the psf does not have entry for the CNTube. So , I've
> > > tried
> > > > to create a residue , but it seems to be wrong though it looks
> > > > alright. Can anybody please let me know how to generate topology
> > > > information (basically bond info) from a pdb file . Also, is there
> > > any
> > > > method of getting a psf from a bgf file ?
> > > >
> > > > Please let me know .
> > > >
> > > > Rgds,
> > > > Prateeksha
> > >
> >
> >
> >
>
>

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