From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Sep 03 2015 - 20:36:45 CDT
Hi Lara,
Your patches probably don’t properly correct the angles and dihedrals. Try adding
regenerate angles dihedrals
after the guesscoord line and it ought to work.
Best,
Peter
> On Sep 3, 2015, at 8:13 PM, Lara rajam <lara.4884_at_gmail.com> wrote:
>
> 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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