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
Received on Wed Apr 08 2009 - 01:19:39 PDT
