You could use g_spatial instead as that program requires you to do the reference calculation yourself with trjconv. I have not tried g_sdf in a while, but if you still would rather use that program, then you might be able to trjconv your own alignment and then somehow fool g_sdf into not doing the alignment, e.g. set all the reference atoms as the same atom?

Chris.

-- original message --

Dear Users,

I want to calculate the spatial distribution function of lipid headgroups around a protein residue. Because I am using a coarse-grained model each 'residue' is a single CG particle. This means that when defining the 3 reference groups that define the local coordinate axes I have no choice but to choose three groups with different residue numbers which I think is causing the program to simply not calculate anything and report zeros. G_sdf runs fine when I test it on systems in which all the reference groups are in the same residue. Is there anyway to post-process my trajectory to fool g_sdf into thinking the reference groups all have the same residue number?

This is the message I get at present:
Reading frame       0 time 180000.000
Warning: reference triple (0) will be skipped.
         resnr[1]: 1862, resnr[2]: 1860, resnr[3]: 1861
Last frame       4000 time 240000.000

Back Off! I just backed up refmol.gro to ./#refmol.gro.1#

Wrote reference structure. (3 Atoms)

Number of configuations used for SDF: 0

Mean probability density: 0.000000

Many thanks,
Rob


_______________________________________________
gmx-users mailing list    gmx-users@gromacs.org
http://www.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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Reply via email to