RE: problems mutating HID to TYR for free energy calculations

From: Radak, Brian K (
Date: Tue Mar 07 2017 - 09:49:38 CST

Hi Nehad,

I do not see your RTF and RES or PRES definition included here. Can you send this?

My guess would be that the IC table is incomplete or missing and thus psfgen cannot guess coordinates. Connectivity might also be a problem, since I don't see any regenerate calls.


Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory

9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
From: [] on behalf of Nehad Elsalamouny []
Sent: Tuesday, March 07, 2017 4:27 AM
Subject: namd-l: problems mutating HID to TYR for free energy calculations

Dear NAMD users,

I am planning to run free energy calculation while mutating HID to TYR. I created h2y.rtf (topology file for histidine to tyrosine transformation). After running psfgen, I get h2y.pdb (attached) with zero coordinates for H2Y segment:

psfgen script used is:

package require psfgen
topology ../../toppar_mass_orig/non_charmm/parm14sb_all.rtf
topology ../../xxxxxx/h2y.rtf

pdbalias atom ILE CD1 CD
pdbalias residue HIS HID

segment H2Y {pdb xxxxx.pdb}
coordpdb xxxxx.pdb H2Y

patch DISU H2Y:62 H2Y:46
patch DISU H2Y:125 H2Y:54
patch DISU H2Y:219 H2Y:150
patch DISU H2Y:198 H2Y:182
patch DISU H2Y:237 H2Y:209

writepdb h2y.pdb
writepsf h2y.psf

I donít know why psfgen doesnít correctly guess missing coordinates?

Original pdb (xxxx.pdb) and output pdb (h2y.pdb) files attached.



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