[gmx-users] MD runs and subsequent error

Erik Marklund 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  
> 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  
> 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
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys

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