Re:

From: Akshay Bhatnagar (akshaybhatnagar2790_at_gmail.com)
Date: Fri Apr 22 2016 - 02:30:13 CDT

I would suggest you to check if your topology file contains TIP3
inforrmation

With Regards
Akshay Bhatnagar
PhD Student
BITS Pilani Hyderabad Campus

On Fri, Apr 22, 2016 at 11:49 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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