From: Tristan Croll (
Date: Tue Oct 06 2015 - 18:44:21 CDT

Hi Siddharth,

(cross-posting to VMD-L because this is more of a VMD question)

>From looking at the files you sent me off-list, you have a few problems here. First up, you need to change your PSFgen script:

 patch SUF6 CT:1
patch NHSHB CT:1

regenerate angles dihedrals


The regenerate... line *has* to come after all patches are applied, because unlike in CHARMM27, CHARMM36 doesn't include angles and dihedrals in patches. Without this line, all atoms changed or added by the patch will be rattling around without *any* angle or dihedral restraints, leading to nonsensical conformations.

Your second problem: your parameter files don't appear to actually include necessary dihedral parameters for these patches, so you have a bit more work to do there.

One other thing: when working with newly-introduced topology files, I think it's best to lead with

psfcontext reset

rather than resetpsf. With the latter, the CHARMM27 topology files (as well as any other topologies you've loaded) will still be loaded in memory - only the details of the last protein you worked on are wiped.



Tristan Croll
Faculty of Health
School of Biomedical Sciences
Institute of Health and Biomedical Engineering
Queensland University of Technology
60 Musk Ave
Kelvin Grove QLD 4059 Australia
+61 7 3138 6443

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On 3 Oct 2015, at 8:39 am, siddharth kamal <<>> wrote:

Dear user's
I am trying to generate the psf and pdb file of heparin. In structure the sulfated amine part is showing problem problem.

Here the psfgen script i am using

package require psfgen
topology top_all36_carb_c.rtf
segment CT {
pdb HPN_1.pdb
coordpdb HPN_1.pdb CT
patch SUF6 CT:1
patch NHSHB CT:1

writepdb final_HP.pdb
writepsf final_HP.psf

please see images in the attachment and try to help me out.

Thanking you

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