Dear Dac,
Thanks a lot, I will try that.
Fabian
--------------------------
Fabian Glaser, PhD
Structural and Computational Biology Unit
The Lorry I. Lokey Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
> On 30 Jun 2022, at 15:20, David A Case <david.case.rutgers.edu> wrote:
>
> On Thu, Jun 30, 2022, Fabian Glaser via AMBER wrote:
>>
>> I am willing to run a peptide in acetonitrile solvent, what is the right
>> procedure to get an equilibrated box with this solvent?
>
> One approach, perhaps not the "right" way:
>
> 1. Use antechamber to create mol2 and frcmod files for a single acetonitrile
> molecule.
>
> 2. Use packmol to create a pdb-format file for a box of these.
>
> 3. Use tleap to load the mol2, frcmod, and pdb files from above. Create
> a parm7/rst7 pair, and equilibrate in the usual fashion.
>
> ...good luck...dac
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 04 2022 - 13:33:54 PDT
