psfgen operation for the C terminal of HSE

From: Shulin Zhuang (shulin.zhuang_at_gmail.com)
Date: Mon Mar 27 2006 - 01:46:57 CST

Dear All,

When I use psfgen program to make the parameter file for my protein, it tell
me that"Warning: failed to set coordinate for atom O HIS:118
A".
In the C terminal is the residue HIS which is aliased to be HSE. The last
two residue in the segments of my protein are HIS.

My command is as follows:
topology top_all22_prot.inp
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD

segment A {
pdb chainA.pdb
}

when I type:
 coordpdb chainA.pdb A

the message arise:
reading coordinates from pdb file gdo_frag0.pdb for segment A
Warning: failed to set coordinate for atom O HIS:118 A

when I further type:
guesscoord
it tells me that:
Warning: poorly guessed coordinate for atom OT1 HSE:118 A
Warning: poorly guessed coordinate for atom OT2 HSE:118 A

Are thes warning normal?

Should I use
segment A {
pdb chainA.pdb
last none
}

--
   Shulin Zhuang
Chemistry Department
Zhejiang University PRC
shulin.zhuang_at_gmail.com

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