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

[Alan Dodd]

Capping peptides is non-trivial, so the error may have been introduced there - certainly the approach you stated is not what I or others have used successfully.  There have been a number of posts discussing how to do this, check the archives.

----- Original Message ----
From: OZGE ENGIN <OZENGIN at KU.EDU.TR>
To: gmx-users at gromacs.org
Sent: Friday, August 24, 2007 10:45:14 AM
Subject: [gmx-users] Unusual structures generated by GENCONF command and resultant minimization problem


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.


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