From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Sat Apr 23 2016 - 23:19:09 CDT
Hi Srijita,
I think the water residues should be defined in the toppar_water_ions.str
file. Could you try including this file?
Best,
Chitrak.
On Fri, Apr 22, 2016 at 1:26 PM, Peter Freddolino <petefred_at_umich.edu>
wrote:
> Silly question — is the TIP3 residue definition present, and not commented
> out, in one of your topology files?
>
> > On Apr 22, 2016, at 2:19 AM, Srijita Paul <srijitap91_at_gmail.com> wrote:
> >
> > Hii
> > I m trying to create a psf file from psfgen.my pdb file contains protein
> > urea and tip3p water.i am trying to do it by spliting the pdb in 3
> > different segment for protein urea and water.but when i m trying to build
> > the segment for water the following error is occuring- UNKNOWN RESIDUE
> TYPE
> > TIP3
> > I m using the following psfgen command-
> > mol load pdb protein_urea2500_wat.pdb
> > set protein [atomselect top protein]
> > $protein writepdb protein.pdb
> > set urea [atomselect top "resname UREA"]
> > $urea writepdb urea.pdb
> > set water [atomselect top water]
> > $water writepdb water.pdb
> > package require psfgen
> > topology top_all36_prot.rtf
> > topology top_all36_cgenff.rtf
> > segment p {
> > first none
> > last none
> > pdb protein.pdb
> > }
> > segment u{
> > pdb urea.pdb
> > }
> > pdbalias atom TIP3 O OH2
> > segment w {
> > auto none
> > pdb water.pdb
> > }
> > after that it is saying unknown residue type TIP3
> > molecule destroyed by fatal error
> >
> > the pdb file is also attached here.
> > sorry for the long massage.eagerly waiting for your kind suggestion.
>
>
>
This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:20:21 CST