Hi,
I am new to generating parameters for ligands. I am trying to generate prmtop and inpcrd file for a compound with 56 atoms. I am using the following commands.
1. antechamber -i UNK.mol2 -fi mol2 -o UNKnew.mol2 -fo mol2 -nc -1 -c bcc
2. UNKnew.mol2 looks fine. An overview of the .mol2 file is shown below
.<TRIPOS>MOLECULE
UNK
56 60 1 0 0
SMALL
bcc
.<TRIPOS>ATOM
1 C 24.9320 6.5800 92.0160 c3 1 UNK 0.383600
2 C1 26.4090 6.6830 92.3710 c3 1 UNK -0.145400
3 C2 26.8330 7.9940 91.7110 c3 1 UNK 0.167100
4 C3 25.8800 8.1470 90.5220 c3 1 UNK -0.081700
.........remaining lines not shown....
.........remaining lines not shown....
26 H 26.5720 6.6810 93.4480 hc 1 UNK 0.076200
27 H1 26.9330 5.8310 91.9360 hc 1 UNK 0.076200
28 H2 26.7040 8.7950 92.4270 h1 1 UNK 0.034700
29 H3 26.1740 7.4340 89.7720 hc 1 UNK 0.139700
.........remaining lines not shown....
.........remaining lines not shown....
.<TRIPOS>BOND
1 1 2 1
2 1 5 1
3 1 6 1
.........remaining lines not shown....
.........remaining lines not shown....
60 25 56 1
.<TRIPOS>SUBSTRUCTURE
1 UNK 1 TEMP 0 **** **** 0 ROOT
3. parmchk -i UNKnew.mol2 -f mol2 -o UNKnew.frcmod
I am getting incomplete frcmod file, which reads as
remark goes here
MASS
BOND
ANGLE
os-c3-o 72.654 116.270 Calculated with empirical approach
DIHE
IMPROPER
NONBON
----I couldn't find any mistake in the input .mol2 file. I went through mailing list and few tutorials, but couldn't find a solution.
Any suggestion/help in this regard is appreciated.
Thanks and regards,
Latha.
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UT Southwestern Medical Center
The future of medicine, today.
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Received on Fri Mar 21 2014 - 11:30:02 PDT
