VMD-L Mailing List

From: Anirban Ghosh (anirbanz83_at_yahoo.co.in)
Date: Mon Oct 20 2008 - 08:30:49 CDT

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> > To: Anirban Ghosh <anirbanz83_at_yahoo.co.in> > Cc: VMD List <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* > > > > > > Send free SMS to your Friends on Mobile from your Yahoo! Messenger. > > Download Now! http://messenger.yahoo.com/download.php > > Send free SMS to your Friends on Mobile from your Yahoo! Messenger. > Download Now! http://messenger.yahoo.com/download.php Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php