VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Oct 20 2008 - 09:04:03 CDT

Hi Anirban,
did you try splitting the segments into separate pdb files and
generating them with separate segment statements, as I suggested?
Peter

Anirban Ghosh wrote:
> Respected Sir,
>
> Sorry for that mistake, I have added the mail list to CC.
> For my molecule the ADE residues which are also having the same atom
> definitions (like C4* in place of C4') as the URA residues, are
> getting considered in the PSF files. But why not for the URA residues?
> Another thing is that the same pdb file when used in the Autopsf
> plugin generates the PSF file with both ADE and URA residues, but not
> in case of the script. Do I need to add any CHARMM Parameter file in
> the script? Please suggest.
>
> Refards,
>
>
>
> *Anirban Ghosh*
> *M.Tech Bioinformatics*
> *University of Hyderabad*
>
>
> ----- Original Message ----
> From: Peter Freddolino <petefred_at_ks.uiuc.edu>
> To: Anirban Ghosh <anirbanz83_at_yahoo.co.in>
> Sent: Monday, 20 October, 2008 6:28:14 PM
> Subject: Re: vmd-l: PSFGEN problem with URA residues
>
> Hi Anirban,
> there are a couple issues here.
> -please reply to the lists when following up on questions to them
> -Your uracil residues have atoms whose names do not match the names in
> the topology file (eg, O5* instead of O5')
> -Your uracil residues are all in a third segment, so you need to split
> your input pdb file into one pdb file for each segment (one for the
> protein, one for each of your two nucleic acid chains, and at least one
> for the water) and generate each segment separately. See the psfgen
> manual for more on this. If you have multiple residues with the same
> number in the same segment, psfgen ignores all but the first; I believe
> this is what is happening to your uracils.
>
> Best,
> Peter
>
> Anirban Ghosh wrote:
> > Respected Sir,
> > Yes I ahve checked for the residue name and it is URA in the pdb file.
> > Infact initially it was U, so I used alias first to generate the PSF
> > file, then I changed U to URA, but every time the URA residues are not
> > considered if I use the script. I am attaching the PDB file also.
> > Please suggest.
> >
> > Regards,
> >
> >
> >
> > *Anirban Ghosh*
> > *M.Tech Bioinformatics*
> > *University of Hyderabad*
> >
> >
> > ----- Original Message ----
> > From: Peter Freddolino <petefred_at_ks.uiuc.edu
> <mailto:petefred_at_ks.uiuc.edu>>
> > To: Anirban Ghosh <anirbanz83_at_yahoo.co.in
> <mailto:anirbanz83_at_yahoo.co.in>>
> > Cc: VMD List <vmd-l_at_ks.uiuc.edu <mailto:vmd-l_at_ks.uiuc.edu>>
> > Sent: Monday, 20 October, 2008 5:29:42 PM
> > Subject: Re: vmd-l: PSFGEN problem with URA residues
> >
> > Hi Anirban,
> > are you sure that the residues are actually named URA in your input pdb?
> > Frequently uracil residues are named U in pdb files, or have some atoms
> > with incorrect naming; autopsf has some aliases that it applies to
> > circumvent common naming problems like this. Your first step should be
> > to make sure that your residue and atom names exactly match those in the
> > topology file.
> > Best,
> > Peter
> >
> > Anirban Ghosh wrote:
> > > Hi ALL,
> > >
> > > I want to generate PSF files for a large no. of PDB files at a time.
> > > My molecules consists of URA residues. When I am generating the PSF
> > > files with the following script, then the URA molecules are not
> > > getting considered in the generated PSF file.
> > >
> > > ###################################
> > > package require psfgen
> > > resetpsf
> > >
> > > topology top_all27_prot_lipid_na.inp
> > >
> > > segment 1 { pdb 1.pdb}
> > > coordpdb 1.pdb 1
> > >
> > > guesscoord
> > >
> > > writepdb 1_new.pdb
> > > writepsf 1_new.psf
> > > ###################################
> > >
> > > However if I use the Autopsf plugin of VMD, then the output PSF files
> > > are having the URA residues. Why is this happening?
> > > I want to use the script as I need to generate a large no. of PSF
> > > files at a time. Please advice what is going wrong in the script.
> > >
> > >
> > > Regards,
> > >
> > >
> > >
> > > *Anirban Ghosh*
> > > *M.Tech Bioinformatics*
> > > *University of Hyderabad*
> > >
> > >
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