On 5/19/13 10:36 PM, David Rosenman wrote:
Hello again,
Sorry for the delay in my response.
The original top file is:
http://wikisend.com/download/951610/APPTM_WT.top
The grompp -pp processed top is:
http://wikisend.com/download/851584/APPTM_WT_processed.top
The connectivities that are not explicitly mentioned in either of these
files are the connections between the second molecule of the homodimer,
between all DPC detergent molecules, and between all water molecules.
GROMACS already knows what the connectivities of these are because it can
interpret both included itp files and multiple molecules. But, top2psf
doesn't.
Or just do it by hand and replace the lines in the .top with each
protein chains .itp file.
This won't work because the generalized atom indices in the itp files don't
match the actual atom indices in the structure for each molecule I need
included. And there are many molecules to deal with here. . .ie, 100000
water molecules! I suppose one could write a script to make the
translation, but it sounds like it may be a challenging task.
If all of your molecules are described by .rtp entries, you can re-run pdb2gmx
on the completed system, applying some suitable option to -chainsep to create
new [moleculetypes] for every molecule present. The topology will be very
redundant, but it may give you what you want.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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