Lauren,
the easiest way to compute the vdW energy between two sets of atoms is
IMO the lie command in cpptraj (see section 36.11.43. in the Amber24
manual), where you specify two masks of atoms, between which the
interaction energy (vdW and/or elec) is then calculated.
Hope that helps.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
Am 13.01.2025 um 21:23 schrieb Intravaia, Lauren E via AMBER:
> Hello,
>
> I am trying to calculate the vdW energy of side chains between residues 1 and 2 throughout the MD trajectory. The command I am using now is pairwise through cpptraj:
>
> pairwise :1,2&!(.N,CA,C,O,H*) out pair_1_2.dat
>
> Is this the best method to calculate pairwise interactions?
>
> Thanks in advance,
> Lauren Intravaia
>
> --
> Lauren Intravaia
> PhD Candidate
> Celia Schiffer Lab
> Dept. of Biochemistry and Molecular Biotechnology
> University of Massachusetts Chan Medical School
> 364 Plantation St. LRB 970D
> Email: lauren.intravaia.umassmed.edu<mailto:lauren.intravaia.umassmed.edu>
> LinkedIn: www.linkedin.com/in/lauren-intravaia<http://www.linkedin.com/in/lauren-intravaia>
> Lab website: https://www.umassmed.edu/schifferlab/
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 14 2025 - 03:30:02 PST
