[gmx-users] Re: Salt-bridge segmentation fault
hmkvsri at gmail.com
Thu Feb 7 13:11:47 CET 2013
I have noticed this in the output of the g_saltbr. Later
I separated the files according to what ever I require.
My worry was only that of the dimeric interface which
could not be seen because it is separated.
I will try by giving a separate tpr file without water.
On Thu, Feb 7, 2013 at 5:31 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 2/7/13 6:42 AM, Kavyashree M wrote:
>> Dear users,
>> After simulation dimers appear separated, I was
>> able to do saltbridge calculation on this. This will
>> be different than doing it on a dimer which are together.
>> Am I correct?
> Most Gromacs tools handle PBC well for simple metrics like measurements.
> I would suspect that the seg fault comes from a mismatch in the .tpr and
> .xtc contents. g_saltbr is a rather stupid tool that tries to guess salt
> bridges based on anything that's charged, which includes ions and other
> groups that don't necessarily participate in such interactions (see the
> discussion on this same topic in recent days). Perhaps if g_saltbr is
> identifying elements that it wants to examine from the .tpr file but can't
> find them in the trajectory, you get a seg fault. This shouldn't happen,
> but you can also use tpbconv to produce a subset .tpr file with just the
> protein for the purposes of analysis.
> On Thu, Feb 7, 2013 at 3:39 PM, Kavyashree M <hmkvsri at gmail.com> wrote:
>> Dear users,
>>> While calculating salt bridges using g_saltbr I got
>>> segmentation fault when I used trajectory with only
>>> the protein. But when I used the trajectory with
>>> water It worked. But the problem was that the
>>> monomers were far apart in the trajectory with water
>>> and not with the only-protein trajectory.
>>> Kindly help!
>>> Thank you
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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