Re:

From: Peter Freddolino (petefred_at_umich.edu)
Date: Fri Apr 22 2016 - 12:26:51 CDT

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.

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