[gmx-users] Minimization of a box of capped tryptophan (trp)

David van der Spoel spoel at xray.bmc.uu.se
Sat Aug 25 20:34:15 CEST 2007

> Hi all, 
> As you suggest David I used genconf command without -rot option. I minimized a single capped trp molecule and got the minimized molecule and used that molecule with genconf command in order to create a box. 
>> Then, I solvated capped trp molecule  within the created box with genbox command. I wanted the box to have a total of 200 capped trp molecules. In this respect, I used -maxsol 200 option. However, the resultant system had only 11 capped trp molecules.
>> What may be the problem?

box too small?

use genconf -nbox 8 5 5 or something like that
> Thanks
> Oz.
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

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

More information about the gromacs.org_gmx-users mailing list