[gmx-users] Fw: pdb2gmx atom not found

xy21hb xy21hb at 163.com
Fri Dec 12 20:43:17 CET 2014

-------- Forwarding messages --------
From: "xy21hb" <xy21hb at 163.com>
Date: 2014-12-13 01:52:03
To:  "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Subject: [gmx-users] pdb2gmx atom not found
Dear all,

I am introducing a residue named ABC into AMBER03 force field. I built up the aminoacids.rtp and aminoacids.hdb file,
but when I pdb2gmx, it gives,
Atom HB1 not found in rtp database in residue ABC, it looks a bit like HB
I am pretty sure I use HB instead of HB1, and there is no atom called HB1 in any of the above-mentioned files.(including .pdb for pdb2gmx)
then I changed my HB to HB1, it gives similar error, 

Atom HB11 not found in rtp database in residue ABC, it looks a bit like HB1

It seems that pdb2gmx is appending the name with "1".

Anyone knows why that is?


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