AMBER Archive (2003)

Subject: Including the Peroidiic Box info ??

From: N. Jiten Singh (jiten_at_postech.ac.kr)
Date: Wed Feb 12 2003 - 21:21:41 CST

Dear Amber Users,

After the MD equilibration of solvent molecules the final .rst (restart) file is converted to pdb (using ambpdb) and load it is xleap and save the file.off . Here the peroidic informations is lost - then I include the peroidic conditios in the !entry boundbox in file.off by putting the box size calculated from the final VOLUME of the equilibration. When I load the file.off in xleap I could see only 1/4 of the solvent space is covered by the periodic box while the original box before starting the equilibration covers the whole solvent space. When I check the solvent boxes provided with Amber it covers the whole solvent space.

My question is that can I use file.off as the solvent box for solavating my system ? Is this the right way of making the solvent BOX from the equilibrated coordinates.

Your kind suggestions would be highly thankful,

Best wishes,

Jiten

N. Jiten Singh
Center for Superfunctional Materials
Department of Chemistry
Pohang University of Science and Technology
San 31, Hyojadong, Namgu
Pohang 790-784, Korea
Phone : 82-54-279-5853 ( Lab )
Fax : 82-54-279-8137 (or +82-54-279-3399)
Web : http://csm.postech.ac.kr/ and http://www.postech.ac.kr/e