Re: [AMBER] antechamber issues

From: <>
Date: Thu, 18 Jul 2013 17:09:49 +0000


thanks for your reply. I want to have Sybyl atom types in the output from a gaff mol2 file. I got those but the wrong ones. I don't think that cc/cd, ss, na should be translated to C.2, S.3, N.3. I would have expected to see, S.2 and as they were original. You see, a ful cycle of backward and forward conversions should not result in different types. But it does.


From: Junmei Wang []
Sent: 18 July 2013 17:55
To: AMBER Mailing List
Subject: Re: [AMBER] antechamber issues


For the first issue, I guess you misunderstand the '-at ' flag as the
atom types of the input file. As a matter of fact, you use '-at' to
specify the atom type of the output file. The default atom type is
'gaff'. So you could get gaff atom types simply running command:

antechamber -i ring.mol2 -fi mol2 -o ring-sybyl.mol2 -fo mol2

For the second issue, please add more stuff immediately after the
following three lines in antechamber.c
        if (strcmp("gesp", cinfo.outtype) == 0
                || strcmp("25", cinfo.outtype) == 0)

stuff you need to add:
        if (strcmp("sqmcrt", cinfo.outtype) == 0
                || strcmp("23", cinfo.outtype) == 0)
                wsqmcrt(ofilename, atomnum, atom, minfo);
        if (strcmp("sqmout", cinfo.outtype) == 0
                || strcmp("24", cinfo.outtype) == 0)
                wsqmout(ofilename, atomnum, atom, cinfo, minfo);

We will also file a bug report soon



On Wed, Jul 17, 2013 at 4:02 AM, Hannes Loeffler
<> wrote:
> Hi,
> I have found two issues with antechamber:
> 1) When I convert the attached pdb file to mol2 with e.g.
> antechamber -i ring.pdb -fi pdb -o ring.mol2 -fo mol2 -j 4 -s 2
> I get a mol2 file with reasonable GAFF atom types.
> But when I try to get a "standard" mol2 with Sybyl atom types via
> antechamber -i ring.mol2 -fi mol2 -o ring-sybyl.mol2 -fo mol2 -at sybyl
> -s 2 -j 4 (or -j 1)
> I get wrong atom types (see attachment). The same happens when
> directly converting from the PDB (identical mol2).
> Converting the original pdb to mol2 with openbabel yield Sybyl atom
> types that I would think are a reasonable match of the GAFF types (see
> attachment).
> 2) I would expect a command like
> antechamber -i ring.pdb -fi pdb -o -fo sqmcrt -j 0
> to write the SQM input file but it doesn't (not output generated at
> all).
> Thanks,
> Hannes.
> --
> Scanned by iCritical.
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Received on Thu Jul 18 2013 - 10:30:02 PDT
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