From: Tristan Croll (tristan.croll_at_qut.edu.au)
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
guesscoord
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.
Cheers,
Tristan
Tristan Croll
Lecturer
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
This email and its attachments (if any) contain confidential information intended for use by the addressee and may be privileged. We do not waive any confidentiality, privilege or copyright associated with the email or the attachments. If you are not the intended addressee, you must not use, transmit, disclose or copy the email or any attachments. If you receive this email by mistake, please notify the sender immediately and delete the original email.
On 3 Oct 2015, at 8:39 am, siddharth kamal <411cy5084_at_nitrkl.ac.in<mailto:411cy5084_at_nitrkl.ac.in>> 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
resetpsf
segment CT {
pdb HPN_1.pdb
}
coordpdb HPN_1.pdb CT
patch SUF6 CT:1
patch NHSHB CT:1
guesscoord
writepdb final_HP.pdb
writepsf final_HP.psf
please see images in the attachment and try to help me out.
Thanking you
Siddharth
<vmdscene3.jpg>
This mail has been scanned by Cyberoam based UTM at NIT, Rourkela. If your mail still contains virus forward it to "spam_at_nitrkl.ac.in<mailto:spam_at_nitrkl.ac.in>"
This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:21:22 CST