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

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Feb 22 2008 - 07:03:16 CST

Hi Prateeksha,
you should not need to specify dihedrals in the topology files, but you
do not to specify impropers explicitly. You can do this with a series of
IMPR atom1 atom2 atom3 atom4
lines in the topology file, enumerating all sets of atoms which should
have impropers. You should look at the existing topology files to see
how these entries are used.

You can verify that the dihedrals and impropers were generated by
looking at the NPHI and NIMPHI headings in your psf file.
Best,
Peter

prateeksha s wrote:
> 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
> <mailto: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
> <mailto: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
> <mailto: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
> <mailto: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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