Re: [AMBER] How to have a certain number of water molecules?

From: David Case <>
Date: Fri, 13 Jan 2017 13:29:43 -0500

On Fri, Jan 13, 2017, Azade Yazdan Yar wrote:
> the problem now is how to get prmtop/inpcrd files from mixtures.pdb in
> xleap?

You load the mol2 and frcmod files into xleap/tleap: this establishes the
"libraries" that tleap needs to create the prmtop files.

Next, this command:

   mixture = loadPdb mixture.pdb

This establishes the unit named "mixture". The residue names in this pdb file
must match the residue names in the mol2 files loaded earlier.

Then do this:

   set mixture box { ...put box dimensions here.... }
   saveAmberparm mixture mixture.parm7 mixture.rst7

> To sum up, my problem is that I have a pdb but I cannot tell xleap where to
> get the mol2/frcmod parametres for it.

tleap automatically looks at the residues and atoms in the mixture.pdb file,
and tries to match them to the residue/atom names in the mol2 files. tleap
will report any problems it has in making this match.

...hope this helps...dac

AMBER mailing list
Received on Fri Jan 13 2017 - 10:30:02 PST
Custom Search