[gmx-users] Unusual structures generated by GENCONF command and resultant minimization problem

[OZGE ENGIN]

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. 

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.