When you make the file with antechamber, I suggest to add the command:
-at amber
Moreover, if you use molden, I also suggest to save the gaussian
output in pdb format directly with molden, and then you can convert
this one in mol2 with antechamber. In this way, I have never had
problems.
Hope this will work.
T.
Def. Quota Enrico Caldarulo <enrico.caldarulo2.studio.unibo.it>:
> Hi,
> I have some problems to parametrize the perchlorate anion.
> I did the following things:
> antechamber -i <name>.pdb -fi pdb -o <name>.com -fo gcrt (Gaussian input)
> antechamber -i <name.log>-fi gout -o <name.mol2> -fo mol2 -c resp
> -nc -1 -m 1 -j full
> antechamber -i <name.mol2> -fi mol2 -o <name.prepin> -fo prepi -j full
> parmchk -i <name.prepin> -f prepi -o <name.frcmod> -j full
> At this point I obtained a frcmod file that is not useful to create
> a parmtop file
> remark goes here
> MASS
> O1 0.000 0.000 ATTN, need revision
> Cl1 0.000 0.000 ATTN, need revision
> O3 0.000 0.000 ATTN, need revision
> O4 0.000 0.000 ATTN, need revision
> O2 16.000 0.434 same as o
>
> BOND
> O1-Cl1 0.00 0.000 ATTN, need revision
> Cl1-O3 0.00 0.000 ATTN, need revision
> Cl1-O4 0.00 0.000 ATTN, need revision
> Cl1-O2 0.00 0.000 ATTN, need revision
>
> ANGLE
> O1-Cl1-O3 0.000 0.000 ATTN, need revision
> O1-Cl1-O4 0.000 0.000 ATTN, need revision
> O1-Cl1-O2 0.000 0.000 ATTN, need revision
> O3-Cl1-O4 0.000 0.000 ATTN, need revision
> O3-Cl1-O2 0.000 0.000 ATTN, need revision
> O4-Cl1-O2 0.000 0.000 ATTN, need revision
>
> DIHE
>
> IMPROPER
>
> NONBON
> O1 0.0000 0.0000 ATTN, need revision
> Cl1 0.0000 0.0000 ATTN, need revision
> O3 0.0000 0.0000 ATTN, need revision
> O4 0.0000 0.0000 ATTN, need revision
> O2 1.6612 0.2100 same as o
>
> Thank you
>
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>
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Received on Fri Jan 21 2011 - 08:30:02 PST
