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

From: prateeksha s (prateeksha.s_at_gmail.com)
Date: Sat Jan 19 2008 - 23:02:22 CST

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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