From: Lara rajam (lara.4884_at_gmail.com)
Date: Thu Sep 03 2015 - 19:13:21 CDT
I am trying to generate the psf and pdb file for heparin !
I under stood the issues with the N sulfated glycan.
as initial i tried idoA 2sulfated and 6 sulfated glucosamine.
I took the pdb from 1HPN ( dimer )
my psfgen as below
package require psfgen
topology top_all36_carb.rtf
resetpsf
segment GT1 {
pdb two.pdb
}
coordpdb two.pdb GT1
patch 14bb GT1:2 CT1:1
patch SUF2B GT1:1
patch SUF6 GT1:2
guesscoord
writepdb dimer.pdb
writepsf dimer.psf
**********************
The psf file is not giving the information about the angle and the dihedral
terms for the SO3 group constituting atoms.
Is there any problem in my patching , how to patch it
( is the sulfate molecules are treated as a separate residues in the PDB
file ? )
could any one can explain me .
thanks in advance !
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