[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

> 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...
> Oz.
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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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