Re:

From: Srijita Paul (srijitap91_at_gmail.com)
Date: Fri Apr 22 2016 - 05:39:12 CDT

yes the topology file top_all36_cgenff.rtf contains TIP3 information.still
the following problem is arising.

On Fri, Apr 22, 2016 at 1:00 PM, Akshay Bhatnagar <
akshaybhatnagar2790_at_gmail.com> wrote:

> 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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