The problem is a mismatch in the contents of the .gro/.xtc and .psf produced by
top2psf.pl. Since the script only handles one moleculetype, you can only
display and/or read coordinates of that same moleculetype. So, to display properly:
1. Strip only the protein's coordinates from the .xtc and fix PBC suitably (the
one you provided me with is not very useful for visualization - the protein is
flying all around)
2. Strip the protein's coordinates from your .gro
3. Load the .gro in VMD, then the .psf as data for it, then the protein-only
.xtc as data for the .gro.
I followed these steps (aside from proper PBC) and your protein loaded just
fine.
-Justin
John wrote:
Thank you for offering help. I know your script is doing it's job, the
problem lies with me. for some reason i cannot figure out where i am
going wrong. i am attempting to look at a 163 residue, 2 domain protein
(hPin1) and this is on of the domains by itself (only 39 residues).
i'm attaching a .gro, .itp, .top, and an .xtc for a short 10ns run. i am
definitely a beginner when it comes to both GROMACS and MARTINI. I am
trying to get a few molecules toward some production simulations with
the MARTINI model. for this domain i have something strange happening
around 3ns. the rmsd for the protein nearly freezes to a straight line.
i am trying to visually see what is going on in the hopes that that
might allow me to figure out what the heck to do next.
i really appreciate your help a lot. i am sort of isolated, lately, from
anyone i can discuss anything regarding simulation issues.
best,
john
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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