Dear Amber Users,
I am using AmberTools17 and try to parameterize a drug like molecule using antechamber and parmchk2 with gaff2. The followings are the commands I use:
antechamber -i Structure3D.sdf -fi sdf -rn LIG -o Structure3D.mol2 -fo mol2 -c bcc -nc 0 -pf yes -dr no -at gaff2
parmchk2 -i Structure3D.mol2 -f mol2 -o Structure3D.frcmod -s 2
The first command finished successfully, however, the second command returned me an error message and an empty frcmod file:
Warning: Atom type (cs) is not in PARMCHK.DAT; using default values
for improper_flag [0], group_id [0], and equivalent_flag [0].
It is recommended to add the new atom type (cs) to PARMCHK.DAT.
Segmentation fault (core dumped)
Is there any suggested way to deal with this?
Many thanks.
Kun-Lin
+++++++ The mol2 file created by the first command +++++++
.<TRIPOS>MOLECULE
LIG
34 35 1 0 0
SMALL
bcc
.<TRIPOS>ATOM
1 S1 -0.7950 1.1620 0.1470 ss 1 LIG -0.028200
2 C1 -2.5140 1.5130 0.2600 cs 1 LIG 0.344000
3 S2 -3.0910 2.9330 0.9180 s 1 LIG -0.293400
4 N1 -3.2390 0.4690 -0.2710 n 1 LIG -0.452400
5 C2 -4.6990 0.3960 -0.2890 c3 1 LIG 0.049000
6 C3 -5.1910 -0.1940 1.0200 c 1 LIG 0.617100
7 O1 -4.5110 -0.6320 1.9350 o 1 LIG -0.530000
8 O2 -6.5380 -0.1960 1.1060 oh 1 LIG -0.605100
9 C4 -2.5190 -0.6190 -0.7320 c 1 LIG 0.710700
10 O3 -2.9950 -1.6390 -1.2120 o 1 LIG -0.566500
11 C5 -1.0610 -0.3770 -0.5710 cc 1 LIG -0.169600
12 C6 -0.1450 -1.2640 -0.9830 cf 1 LIG 0.013000
13 C7 1.3030 -1.1260 -0.8920 cf 1 LIG -0.108200
14 C8 1.9960 -1.0390 -2.2260 c3 1 LIG -0.064900
15 C9 1.9120 -1.0890 0.3090 ce 1 LIG -0.056200
16 C10 3.3520 -0.9330 0.5320 ca 1 LIG -0.074800
17 C11 3.8320 0.2710 1.0550 ca 1 LIG -0.110500
18 C12 5.1970 0.4400 1.2920 ca 1 LIG -0.132000
19 C13 6.0880 -0.5950 1.0090 ca 1 LIG -0.118000
20 C14 5.6160 -1.8010 0.4910 ca 1 LIG -0.132000
21 C15 4.2490 -1.9710 0.2550 ca 1 LIG -0.110500
22 H1 -5.1270 1.3930 -0.4180 h1 1 LIG 0.116700
23 H2 -5.0310 -0.2510 -1.1070 h1 1 LIG 0.116700
24 H3 -6.7260 -0.5950 1.9830 ho 1 LIG 0.451000
25 H4 -0.4810 -2.1800 -1.4710 ha 1 LIG 0.160000
26 H5 1.5480 -0.2480 -2.8380 hc 1 LIG 0.051700
27 H6 3.0610 -0.8080 -2.1430 hc 1 LIG 0.051700
28 H7 1.9020 -1.9870 -2.7670 hc 1 LIG 0.051700
29 H8 1.3310 -1.1550 1.2270 ha 1 LIG 0.136000
30 H9 3.1460 1.0860 1.2780 ha 1 LIG 0.137000
31 H10 5.5610 1.3790 1.6990 ha 1 LIG 0.135500
32 H11 7.1500 -0.4620 1.1960 ha 1 LIG 0.135000
33 H12 6.3130 -2.6080 0.2760 ha 1 LIG 0.135500
34 H13 3.8890 -2.9170 -0.1420 ha 1 LIG 0.137000
.<TRIPOS>BOND
1 2 1 1
2 3 2 2
3 4 2 1
4 5 4 1
5 6 5 1
6 7 6 2
7 8 6 1
8 9 4 1
9 10 9 2
10 11 9 1
11 11 1 1
12 12 11 2
13 13 12 1
14 14 13 1
15 15 13 2
16 16 15 1
17 17 16 ar
18 18 17 ar
19 19 18 ar
20 20 19 ar
21 21 20 ar
22 21 16 ar
23 5 22 1
24 5 23 1
25 8 24 1
26 12 25 1
27 14 26 1
28 14 27 1
29 14 28 1
30 15 29 1
31 17 30 1
32 18 31 1
33 19 32 1
34 20 33 1
35 21 34 1
.<TRIPOS>SUBSTRUCTURE
1 LIG 1 TEMP 0 **** **** 0 ROOT
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Received on Mon Aug 07 2017 - 18:00:02 PDT
