problems mutating HID to TYR for free energy calculations

From: Nehad Elsalamouny (
Date: Tue Mar 07 2017 - 04:27:28 CST

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 don’t know why psfgen doesn’t correctly guess missing coordinates?

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



This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:09 CST