Input mol2 file for parmchk usually includes Amber atom types. It
seems that you got your mol2 fil not with the use of antechamber, thus
it contains unknown atom types such as "C.ar" for example. Try to use
antechamber to create mol2. Note that both antechamber and parmchk
could look for parameters (atom types, force constants, etc.) in
various force fields (GAFF, ff99SB, etc., default is GAFF), see the
program options in manual.
On Wed, Jan 26, 2011 at 12:49 PM, <poll.chemie.uni-hamburg.de> wrote:
> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Dmitry Nilov,
Lomonosov Moscow State University
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Received on Wed Jan 26 2011 - 02:30:03 PST
