[gmx-users] Unusual structures generated by GENCONF command and resultant minimization problem
David van der Spoel
spoel at xray.bmc.uu.se
Sat Aug 25 12:45:15 CEST 2007
OZGE ENGIN wrote:
> Hi gromacs-users,
> I want to simulate a box of that is composed of capped (ACE and NME to N and C termini, respectively) tryptophan molecules.
> As a first stage, I minimized single capped trp molecule, and then used it with genconf command along with the options -rot ans -nbox.
try without -rot
the capping is not a problem if the force field supports it and if you
have succesfully minimized a monomer that seems to be fine in this case.
> In this case, I changed the gro file of capped trp molecule such that it was treated as a single molecule rather than three (cappes and the trp molecule itself). (It was necessary to be able to use that molecule with genconf command.)
> After that, I could obtain a box of trp molecules. However, when I looked at it by using VMD, I saw that some of them had unusual bonds.
> So it caused not to minimization of my system. The steepest descent minimization was terminated before the desired criterion was reached.
> Although I used a minimized capped trp molecule with genconf command, the resultant box contained some trp molecules that have unusual structures. How can I overcome that problem?
> Thanks in advance...
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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