Hi,
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 C.ar, S.2 and N.ar as they were original. You see, a ful cycle of backward and forward conversions should not result in different types. But it does.
Cheers,
Hannes.
________________________________________
From: Junmei Wang [junmwang.gmail.com]
Sent: 18 July 2013 17:55
To: AMBER Mailing List
Subject: Re: [AMBER] antechamber issues
Hello,
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)
wgesp();
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
Best
Junmei
On Wed, Jul 17, 2013 at 4:02 AM, Hannes Loeffler
<Hannes.Loeffler.stfc.ac.uk> 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 sqm.in -fo sqmcrt -j 0
>
> to write the SQM input file but it doesn't (not output generated at
> all).
>
>
> Thanks,
> Hannes.
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Received on Thu Jul 18 2013 - 10:30:02 PDT
