Hi,
Did you watch out for the wrong-hydrogen-in-DNA-termini-error when
using pdb2gmx with amberXX? I can't see that this would cause NaN-
energies, but it may be worth looking into.
/Erik
2 maj 2007 kl. 11.06 skrev Joern Lenz:
dear gromacs users,
i have the following problem:
i performed an md simulation of a complex of protein and DNA (not
covalently
linked) in a box of amber03_tip4p waters and the amber03 forcefield.
evereything is fine and i used the gromacs toools to extract a
certain frame
out of the trajectory file, writing it into a pdb file.
now i used pdb2gmx -merge to merge the chains in the system, since
one strand
of the DNA and the protein were recognized to be chain A, the other
DNA
strand was chain B.
I want to have the protein and the DNA in one molecule to be able
to introduce
distance restraints between certain atoms of the DNA and the protein.
running pdb2gmx and grompp aftreward run without any warnings or
errors.
unfortunately the following energy minimization does not succeed
because of
potenetial energy being "nan". also an md run does not succeed, giving
warnings about LINCS errors.
my question ow is how that can be, i mean i extracted the pdb from
the trr
file (see above) ?!?!
Is there another way to circumvent the way of doing pdb2mgx and
grompp with
the trr-extracted pdb file to get rid of the error (nan and LINCS)
and also
be able to say gromacs that DNA and protein are one molecule to
then be able
to introduce distance restarints in the system between DNA and
protein ???
thanks a lot in advance for your advice. i hope that i soon can go
on with my
work.
greetings from warm and sunny hamburg
joern
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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
[EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys
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