Re: [AMBER] Use leaprc.ff99SB force field

From: Jan Wahl <>
Date: Fri, 14 Jan 2011 16:40:57 +0100

Hello and sorry for the minimum on information

i'm using self-made molecules e.g chains of amino acids or small organic molecules. Therefore i just wantetdto check if the results will differ from my former calculations.

to build the molecules im using MOLDEN to generate the .mol2-file

as far as i understand you correct,
i should use the leaprc.gaff force field ( or is there any other good force field??)

Also i should use the generated .mol2 by antechamber for parmchk???

Thank you for your help

Jan Wahl

Am 14.01.2011 um 16:12 schrieb David A. Case:

> 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
> more.
>> 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
> information.
> ...good luck...dac
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Received on Fri Jan 14 2011 - 08:00:03 PST
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