[gmx-users] G_SDF if reference atoms are in different residues

Hawtin R. R.Hawtin at soton.ac.uk
Wed Aug 27 11:10:09 CEST 2008

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,

Dr Robert Hawtin
Post-Doctoral Research Assistant
School of Chemistry
University of Southampton
Southampton    SO17 1BJ
U.K.        R.Hawtin at soton.ac.uk

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