Hi everyone,
I have to do Molecular Dynamics Simulations of a FE2S2 center containing protein. I need to generate the FE2S2.mol2 and FE2S2.frcmod files.
I have used the antechamber and parmchk for the generation of mol2 and frcmod files. I have run this following command for the generation of mol2 file:-
antechamber -fi pdb -fo mol2 -i FES_H_renum.pdb -o FES.mol2 -c bcc -pf y -nc 0
The mol2 generated file is as:-
@MOLECULE
FES
4 0 1 0 0
SMALL
bcc
@ATOM
1 S1 -12.5580 51.4880 8.6310 S.3 1 FES 0.046000
2 S2 -10.7680 54.1120 9.2520 S.3 1 FES 0.046000
3 FE1 -12.8160 53.6610 8.6150 F 1 FES -0.046000
4 FE2 -10.5580 51.9350 9.4010 F 1 FES -0.046000
@BOND
@SUBSTRUCTURE
1 FES 1 TEMP 0 **** **** 0 ROOT
Command for the generation of frcmod file:-
parmchk -i FES.mol2 -o FES.frcmod -f mol2
FES.frcmod file is :-
remark goes here
MASS
S.3 0.000 0.000 ATTN, need revision
F 19.000 0.320 same as f
BOND
ANGLE
DIHE
IMPROPER
NONBON
S.3 0.0000 0.0000 ATTN, need revision
F 1.7500 0.0610 same as f
I did not get why I got this error of ATTN need revision in frcmod file.
I have attached the mol2 and frcmod files.
I am not able to understand what I have to modify in FES.pdb or FES.mol2 for the generation of frcmod file so that i can further use it in MD simulation.
Thank you in advance.
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