AMBER Archive (2007)

Subject: AMBER: five-coordinated phosphorus

From: Yubo Fan (cpwnome2_at_hotmail.com)
Date: Sat Nov 17 2007 - 08:19:06 CST

Hello,I need to include a five-coordinated phosphorus compound in my simulations. The geometry and esp were calculated by using Gaussian 03. But when I tried to prepare the prepin file, antechamber failed to generate ac files.The error message is:Warning: the assigned bond types may be wrong, please :(1) double check the structure (the connectivity) and/or(2) adjust atom valence penalty parameters in APS.DAT, and/or(3) increase MAXVASTATE in define.h and recompile bondtype.C(4) increase PSCUTOFF in define.h and recompile bondtype.C Be cautious, use a large value of PSCUTOFF (>10) will significantly increase the computer timeError: cannot run '/opt/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full' in judgebondtype() of antechamber.c properly, exitI tried to edit the APS.DAT but I really don't understand the meaning of the columns in the file. I don't need to add a new atom type to the gaff. I can create a seperate force field file on my own. I only need the prepin file even if the atom type for the five-coordiated phosphorus is the same as that for phosphate.Any advice?Regards,Yubo FanChemistry Dept.TAMU
_________________________________________________________________
You keep typing, we keep giving. Download Messenger and join the i’m Initiative now.
http://im.live.com/messenger/im/home/?source=TAGLM
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu