From: Srijita Paul (srijitap91_at_gmail.com)
Date: Fri Apr 22 2016 - 01:19:21 CDT
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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