[gmx-users] Unusual structures generated by GENCONF command and resultant minimization problem
OZENGIN at KU.EDU.TR
Fri Aug 24 11:45:14 CEST 2007
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.
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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