Dears:
As described in AMBER 2016 Manual (Page 274):" parmchk2 reads in an ac/mol2/prepi/prepc file, an atomtype similarity index file (the default is $AMBERHOME-/dat/antechamber/PARMCHK.DAT) as well as a force field file (the default is $AMBERHOME/dat/leap/parm/-gaff.dat). It writes out a force field modification (frcmod) file containing any force field parameters that are needed for the molecule but not supplied by the force field (*.dat) file. Problematic parameters, if any, are indicated in the frcmod file with the note, ¡°ATTN, need revision¡±, and are typically given values of zero."
When I use parmchk2 to generate frcmod file as following:
parmchk2 -i SeON.mol2 -f mol2 -o SeON.frcmod -s 2
I got a bempty SeON.frcmod file with error infomation :
Atom type of M1 does not shown up in PARMCHK.DAT
Question: How can I generate SeON.frcmod file with the note, ¡°ATTN, need revision¡±, and are typically given values of zero
My SeON.mol2 file :
.<TRIPOS>MOLECULE
SEO
13 13 1 0 0
SMALL
No Charge or Current Charge
.<TRIPOS>ATOM
1 SE 2.7480 5.6950 7.0770 M1 1 SEO 0.000000 (since SE have no Force Filed in GAFF, So I changed as M1)
2 C2 -0.8120 3.9700 5.7310 ca 1 SEO 0.000000
3 C3 0.4230 4.6140 5.7780 CA 1 SEO 0.000000
4 C4 1.0880 4.7460 7.0010 CA 1 SEO 0.000000
5 C5 0.5230 4.2330 8.1730 CA 1 SEO 0.000000
6 C6 -0.7090 3.5850 8.1170 CA 1 SEO 0.000000
7 C7 -1.3760 3.4550 6.8980 CA 1 SEO 0.000000
8 H8 -1.3340 3.8670 4.7790 HA 1 SEO 0.000000
9 H9 0.8770 5.0140 4.8700 HA 1 SEO 0.000000
10 H10 1.0540 4.3420 9.1200 HA 1 SEO 0.000000
11 H11 -1.1500 3.1810 9.0290 HA 1 SEO 0.000000
12 H12 -2.3420 2.9500 6.8590 HA 1 SEO 0.000000
13 I13 4.3490 3.7270 6.8970 I 1 SEO 0.000000
.<TRIPOS>BOND
1 1 4 1
2 1 13 1
3 2 3 1
4 2 7 2
5 2 8 1
6 3 4 2
7 3 9 1
8 4 5 1
9 5 6 2
10 5 10 1
11 6 7 1
12 6 11 1
13 7 12 1
.<TRIPOS>SUBSTRUCTURE
1 SEO 1 TEMP 0 **** **** 0 ROOT
Thanks very much
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Received on Wed Mar 15 2017 - 07:30:02 PDT
