AMBER Archive (2007)

Subject: AMBER: contacts in ptraj (Amber 9)

From: rebeca_at_mmb.pcb.ub.es
Date: Wed Feb 21 2007 - 12:56:50 CST

Hello,
anybody know if would it be possible to calculate the contacts between 2
monomers in a dimer using the ptraj command "contacts" included in Amber 9?

The syntax of this command is

contacts [first/reference] [byresidue] [out filename] [time interval]
[distance
cutoff] [mask]

What should I take as "mask"??

Thanks for your help in advance!

Rebeca García
Parc Cientific Barcelona
rebeca_at_mmb.pcb.ub.es

Quoting rebeca_at_mmb.pcb.ub.es:

> Hello,
> I have performed a molecular dynamics of a protein with NAMD/Charmm. Is it
> possible to analyze the last structure or the trayectory with the ANAL module
> of AMBER using a psf file instead a top file? I could do ptraj using psf, but
> is it possible do the same for ANAL?
>
> Thanks a lot in advance!
>
>
> Rebeca
> rebeca_at_mmb.pcb.ub.es
> Parc Cientific Barcelona
>
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