VMD-L Mailing List

From: Bryan Roessler (roessler_at_uab.edu)
Date: Wed Dec 14 2011 - 11:20:25 CST

Hello,

I generally use about 5-6 stream files in conjunction with top_all36_lipid
and top_all27_protein_na topology files. It seems that I have to guess the
best order to call these files in psfgen or autopsf, otherwise the program
will abort because of missing residue topologies (even though they exist in
the stream files). Is there a de facto order I should placing these in so I
can avoid this problem?

For example:

top_all36_lipid.rtf
top_all27_protein_na.rtf
toppar_all27_na_nad_ppi.str
toppar_prot_na_all.str
custom.str
solvent.str

will fail, but

top_all36_lipid.rtf
top_all27_protein_na.rtf
solvent.str
custom.str
toppar_prot_na_all.str
toppar_all27_na_nad_ppi.str

will work fine.

Ideas?

Thanks,

Bryan Roessler
The University of Alabama at Birmingham