AMBER Archive (2009)

Subject: Re: [AMBER] specification of antechamber AC file format?

From: Nicholas Musolino (musolino_at_MIT.EDU)
Date: Tue Apr 07 2009 - 14:43:57 CDT

Thanks very much, Dr. Case, for your reply. Sorry for the delay in
replying myself.

The issue is not an immediate failure parmchk, in the sense that an
error message returns. Rather, I get zero parameters with an ATTN
remark in the FRCMOD file.

Basically, what I would like to do is a direct "translation" of a
SYBYL MOL2 file to an ac file, while accomplishing the following:
(i) convert SYBYL atomtypes in original file to GAFF atomtypes
(ii) convert SYBYL atom names to non-duplicative atom names (e.g. C1,
C2, ..., C6...)
(iii) retain bonding information from original MOL2 file

Item (iii) is the one I'm having problems accomplishing. I'm trying
to do this in an automated way, and the way I am running antechamber,
it is doing the bond perception on its own, with an error rate of
16/100. Of course, since I have trustworthy bond information, it
doesn't make sense to have antechamber perceive this information from
scratch.

Ultimately, I'd like to generate a prmjoin file from (1) a MOL2 file
that has GAFF atomtypes and non-duplicated atom names, and (2) an
FRCMOD file generated from PARMCHK. If I run parmchk on my MOL2 file
I get lots "ATTN" lines with DU atomtypes and 0.000 force constants,
as I mentioned above.

I've tried doing this in two ways:
Approach I:
antechamber -i orig916_ws.mol2 -fi mol2 -o orig916.prepi -fo prepi -j
5 -at sybyl -nc 0 -c bcc -s 2
Then run PARMCHK on prepin file to generate frcmod file, then use
TLEAP to generate prmjoin file.

Approach II:
antechamber -i orig916_ws.mol2 -fi mol2 -o orig916.ac -fo ac -j 0 -at
sybyl
This creates an ac file with no bond information.

Are there any suggestions for this?

Below is a copy of a sample MOL2 file. I've also included this as an
attachment if that is easier.

@<TRIPOS>MOLECULE

36 36
SMALL
NO_CHARGES

@<TRIPOS>ATOM
  1 C1 4.974300000000 0.882800000000 2.132900000000 C.3
  2 C2 3.594800000000 1.434000000000 2.136900000000 C.2
  3 C3 2.877400000000 1.528900000000 0.942400000000 C.2
  4 C4 3.009100000000 1.870800000000 3.325500000000 C.2
  5 C5 1.592100000000 2.057100000000 0.939600000000 C.2
  6 C6 1.722500000000 2.398100000000 3.318700000000 C.2
  7 C7 1.012700000000 2.492900000000 2.127000000000 C.2
  8 H8 5.685700000000 1.631300000000 1.757900000000 H
  9 H9 5.304700000000 0.587100000000 3.137300000000 H
10 H10 5.051500000000 0.000000000000 1.484500000000 H
11 H11 3.332400000000 1.184400000000 0.007300000000 H
12 H12 3.564600000000 1.797500000000 4.267300000000 H
13 H13 1.034900000000 2.129500000000 0.000000000000 H
14 H14 1.269000000000 2.738800000000 4.255200000000 H
15 H15 0.000000000000 2.908400000000 2.123200000000 H
16 C1 6.401721179114 -1.082774562566 2.714366712210 C.3
17 C2 6.404363300257 0.311396672345 2.128753386762 C.3
18 C3 6.959043342867 0.325362986740 0.722081768226 C.3
19 H4 7.414703646229 -1.504022346318 2.758995357736 H
20 H5 5.789502601937 -1.771041952845 2.116522933922 H
21 H6 5.999123580514 -1.087509820755 3.735223857422 H
22 H7 6.953394396476 1.338093015207 0.299345740845 H
23 H8 6.372037180439 -0.314618132457 0.049913766650 H
24 H9 7.995343413380 -0.036892039577 0.692978507891 H
25 C 7.227483569330 1.254547530194 3.025714635635 C.2
26 O 6.765019709299 1.763289710124 4.029240655490 O.2
27 C1 8.674971450570 1.510092247705 2.566284846641 C.3
28 H2 8.640012931588 1.737628537252 1.492856344649 H
29 C3 9.564267233564 0.331398827576 2.854852709880 C.3
30 H4 10.596835232476 0.514060210895 2.529708823781 H
31 H5 9.596746676402 0.102221867237 3.927820363932 H
32 H6 9.216305333549 -0.573334592921 2.339593256813 H
33 C 9.165129673061 2.780373747920 3.285819298308 C.2
34 O 8.873656942356 3.901219591605 2.603048054077 O.3
35 O 9.752439246890 2.911292678755 4.337178227522 O.2
36 H 9.181579508884 4.680669783976 3.057707399780 H
@<TRIPOS>BOND
  1 1 2 1
  2 1 8 1
  3 1 9 1
  4 1 10 1
  5 2 3 2
  6 2 4 1
  7 3 5 1
  8 3 11 1
  9 4 6 2
10 4 12 1
11 5 7 2
12 5 13 1
13 6 7 1
14 6 14 1
15 7 15 1
16 16 17 1
17 16 19 1
18 16 20 1
19 16 21 1
20 17 18 1
21 18 22 1
22 18 23 1
23 18 24 1
24 1 17 1
25 25 26 2
26 17 25 1
27 27 28 1
28 27 29 1
29 29 30 1
30 29 31 1
31 29 32 1
32 25 27 1
33 33 35 2
34 33 34 1
35 34 36 1
36 27 33 1



On Mar 4, 2009, at 5:39 PM, David A. Case wrote:

> On Tue, Mar 03, 2009, Nicholas Musolino wrote:
>>
>> As a matter of fact, I have MOL2 files with SYBYL atom names and
>> complete bond information, which I generate in an automated way.
>> But no
>> matter what I try, I can't seem to do a straight conversion of this
>> information to .AC format through antechamber. (I also want to add
>> partial charges, but that's not a huge problem.)
>
> Can you provide an example that fails?
>
>>
>> Right now I am looking to bypass antechamber and write my own .AC
>> files
>> for use with parmchk.
>
> It's not clear why you need to write .ac files, which are not really
> intended as a general file format (and it would be good to get rid of
> them). The parmchk program can use mol2 files as input, and you
> seem to
> already have them. Of course, parmchk doesn't know about the sybyl
> force field, so you do need to use antechamber to convert the atom
> types.
>
> Which returns us to the original question -- what is going wrong with
> Antechamber itself?
>
> ...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber


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