From: Lara rajam (lara.4884_at_gmail.com)
Date: Thu Sep 03 2015 - 22:45:34 CDT
Dear Peter !
It worked for me ! the sulfates are now ok
thank you !
On Thu, Sep 3, 2015 at 9:36 PM, Peter Freddolino <petefred_at_umich.edu> wrote:
> 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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