[gmx-users] MD runs and subsequent error
erikm at xray.bmc.uu.se
Wed May 2 11:19:53 CEST 2007
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.
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
> 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
> 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
> 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
> greetings from warm and sunny hamburg
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Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
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phone: +46 18 471 4537 fax: +46 18 511 755
erikm at xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys
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