From: prateeksha s (prateeksha.s_at_gmail.com)
Date: Wed Dec 19 2007 - 22:21:44 CST
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
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.
> 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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