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
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Received on Fri Jan 13 2017 - 10:30:02 PST
