On 14/03/2010 7:47 PM, Andrei Neamtu wrote:
Hi,

is there a rapid way to compute RMSF on an NMR ensemble from a PDB file?

Yes, but that's not your problem, it seems :-)

g_rmsf needs a .tpr file.

Not true. Inspect the lines in g_rmsf -h describing the file types suitable for -f and -s. This is a fairly general GROMACS phenomenon.

This is OK with the MD trajectories but if I
want to compare MD ensemble one with the NMR RMSF ensemble
fluctuations from the original PDB this is not possible.

That can be a trickier proposition. You need at least the atom order to correspond to make such a comparison.

If the original atom names are suitable for defining the default groups, then you might be in business. Otherwise, you'll need to construct suitable input for -s (and maybe -n), and see if it matters whether different atom names in -f matter.

Mark
--
gmx-users mailing list    gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Reply via email to