AMBER Archive (2008)

Subject: AMBER: problem with prep file generation

From: aneesh cna (aneeshcna_at_gmail.com)
Date: Wed Aug 13 2008 - 07:05:58 CDT

Dear Amber Users,

 I am facing a problem with generating prep file. My system contains two
separate molecule (say X and Y). When I am making a prep file separately for
each molecule ,it went fine ( Here I am using two different gaussian outputs
i.e.,X.log and Y.log). But when I am trying to generate a prep file for two
molecule together ( considering X and Y together as a single molecule)
using gaussian output XY.log , prep file contain information about only one
molecule and NEW.PDB also contain coordinates of this molecule (not the
other molecue,say Y). Why its not considering the second molecule even
though I used the option '-j 5' ( i used this option because it showed the
error ' For atom[1] the best APS is not zero, exit' )?. Is there anyway to
generate a prep these two molecule together?

Thanks in advance
Aneesh

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