[gmx-users] Re: Variable ci yet-Samuel's problem!
David van der Spoel
spoel at xray.bmc.uu.se
Tue Aug 15 09:18:50 CEST 2006
Samuel Silva Pita wrote:
> Dear Mr. Spoel,
> i'd described before at GMX lists that my topology of FAD was built by hand and using the atoms adequately for FF G53a6 at GMX 3.3.1. After the addition of atoms , bonds, constants ,etc. at ffg53a6.atp, ffg53a6.hbd and all others arquives, I proceed to minimise the energy if my "system". Converting through pdb2gmx I generate my FAD.gro arquive;I made the configuration of the box -editconf- and made the solvated box, genbox. Despite it alll the error related at ancient e-mails comes again relating a problem at Variable ci. Esther -at GMX list- told me that it could be some superposition of certain atoms and I see that it's truth. But now GMX 3.3.1 does not have any overlaping atoms and the problem remain. I've tried to do genbox using ancient GMX versions and the problem remains.
> Could you give me some sugestions how to treat this problem? I've to do more 21 topologies at GMX and this problem is boring me!
> Samuel Pita.
> "Do not wear yourself out to get rich;do not trust your own cleverness. Cast but a glance at riches, and they are gone, for they will surely sprout wings and fly off to the sky like an eagle."(Proverbs 23:4-5)
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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