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
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