Justin A. Lemkul wrote:
Hi all,
I have noticed that there is a problem with the NH2 directive in
ffG53a5.rtp and ffG53a5.rtp. The following lines are incorrect:
Edit: that should read "ffG53a5.rtp and ffG53a6.rtp"
-Justin
[ impropers ]
-C -O N -CA gi_1
N H H -C gi_1
They refer to the H atoms by type, not name. They should instead read:
[ impropers ]
-C -O N -CA gi_1
N H1 H2 -C gi_1
If the user runs pdb2gmx on a structure containing NH2 they will get a
fatal error:
"Atom H not found in residue 17 while adding improper"
I find that this typo has been present at least since version 3.3, and
remains in version 4.0.5.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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