Dear Fabian,
Yes, we have done it recently (
https://pubs.acs.org/doi/full/10.1021/jacs.9b13029). Initially, we prepared
the parameters for acetonitrile using antechamber of a QM optimized
geometry. I compared it with previously published parameters and it was
almost the same (charge, bond length, force constants etc). Thereafter1 we
used Packmol to produce a solvent box. However, our intention was to study
the effect of applied electric field on this system which worked well.
However, if you are not fond of packmol, there is an alternative way using
tleap.
#load mol2 of acetonitile (ACN) generated from antechamber and then use it
as solvent box instead of TIP3PBOX or SPCBOX, eg.,
ACE=loadmol2 ACE.mol2
solventBox mol ACE 10.0
Best
Kshatresh
On Thu, Jun 30, 2022 at 1:52 PM Fabian Glaser via AMBER <amber.ambermd.org>
wrote:
> Dear experts,
>
> I am willing to run a peptide in acetonitrile solvent, what is the right
> procedure to get an equilibrated box with this solvent?
>
> Did anybody do this in the past?
>
> Thanks a lot in advanced.
>
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Best regards
*************************************************************************************
Dr. Kshatresh Dutta Dubey,
Asst. Professor and Ramalingaswami Fellow
Department of Chemistry, School of Natural Sciences
Shiv Nadar University Delhi-NCR,
India.
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Received on Thu Aug 04 2022 - 13:33:58 PDT
