Please update PARMCHK.DAT in $AMBERHOME/dat/antechamber by adding the
following two lines:
PARM cs 1 0 12.01 0 6
EQUA c
So the updated PARMCHK.DAT looks like:
...
CORR ch 5.1 22.7 0.4 0.5 0.1 0.8 0.1 -1.0 19.3
#
PARM cs 1 0 12.01 0 6
EQUA c
#
PARM H 0 0 1.008 0 1
...
All the best
Junmei
On Mon, Aug 7, 2017 at 8:51 PM, Tsai Kun-Lin <orange6318.hotmail.com> wrote:
> 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 Tue Aug 15 2017 - 05:00:02 PDT
