Re: [AMBER] Use leaprc.ff99SB force field

From: David A. Case <>
Date: Fri, 14 Jan 2011 10:12:45 -0500

On Fri, Jan 14, 2011, Jan Wahl wrote:
> i did all my calculations with the default force field LEAPRC.GAFF
> but now i wanted to do some calculations with differnet force fields e.g
> ff99SB.

Is your system a protein or a nucleic acid? If not, it doesn't make good
sense to use ff99SB.

> antechamber -i input.mol2 -fi 2 -o in.mol2 -fo 2

Look at the "in.mol2" file; I doubt that it is much different from the input
file. See if it has gaff atoms types (lower case).

> and pamrchk :
> parmchk -i ANTECHAMBER_AC.AC -f ac -o frctop

Check the output carefully. As far as I can see, parmchk doesn't even have a
"-f ac" option. I'm not sure what you will be getting, nor do I understand
why you are using ANTECHAMBER_AC.AC as your input file. The various
ANTECHAMBER* files are intermediates that mainly intended for debugging.

> using tleap
> source leaprc.ff99SB
> .
> The manual told me to use the flag -at in antechamber and with this
> command i was able to create a prmtop.

It may be that all of the parameters you need are already in parm99.dat;
without knowing what sort of molecule you are working on, it's hard to say

> To check the results i did a calculation using the same structure but
> now i used a pdb-file to create the prmtop.

You have to examine your various files. Mol2 files already have atom types in
them, so antehcamber may be keeping those. When a pdb file is input,
antechamber has to generate atom types.

> after the calculation the result is different...

Of course, people on the list can't be expected to help much with so little

...good luck...dac

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Received on Fri Jan 14 2011 - 07:30:03 PST
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