[AMBER] Query regarding parmchk

From: <poll.chemie.uni-hamburg.de>
Date: Wed, 26 Jan 2011 10:49:57 +0100

Hi everybody,

I'm pretty new to AMBER. Yesterday I tried the antechamber tutorial
which worked fine with the given example. So wanted to do this again
with some other molecule (attached). It pretty much works until I
want to use the parmchk command to get the frcmod-file. Then I get an
infinite loop in the frcmod-file lookin' like this:

MASS
N.am 0.000 0.000 ATTN, need revision
H 1.008 0.161 same as hn
C.2 0.000 0.000 ATTN, need revision
C.3 0.000 0.000 ATTN, need revision
C.ar 0.000 0.000 ATTN, need revision
N.pl3 0.000 0.000 ATTN, need revision
O.2 0.000 0.000 ATTN, need revision

BOND
N.am-H 0.00 0.000 ATTN, need revision
N.am-C.2 0.00 0.000 ATTN, need revision
C.2-C.3 0.00 0.000 ATTN, need revision
C.2-O.2 0.00 0.000 ATTN, need revision
C.3-H 0.00 0.000 ATTN, need revision
  -N.pl3 0.00 0.000 ATTN, need revision
N.am-H 0.00 0.000 ATTN, need revision
  -N.pl3 0.00 0.000 ATTN, need revision
N.am-H 0.00 0.000 ATTN, need revision
  -N.pl3 0.00 0.000 ATTN, need revision
N.am-H 0.00 0.000 ATTN, need revision
  -N.pl3 0.00 0.000 ATTN, need revision
N.am-H 0.00 0.000 ATTN, need revision
  -N.pl3 0.00 0.000 ATTN, need revision

So I checked the atom types in SYBYL and checked the mol2 file using
acdoctor. This invastigations told me everything is fine and there
should be no problem. Maybe some of you finds the mistake(s).

Thanks in advance

Bernhard

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Received on Wed Jan 26 2011 - 02:00:02 PST
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