[AMBER] Antechamber problems.

From: Steve Seibold <seibold.chemistry.msu.edu>
Date: Thu, 25 Mar 2010 13:44:18 -0400

Bill, Thanks for the email.

To make sure I was understanding the whole process, I went to create a "prepin" file to use in crdgrow using antechamber with a known test case.

I began with the AMBER-supplied test file "tp.pdb". I attempted to run antechamber using this file with the following script also supplied in the AMBER8 manual:

> antechamber -i tp.pdb -fi pdb -o tp.mol2 -fo mol2 -c bcc

I did get some output files (but not a tp.mol2 file) but the error I got said: "/home/.../amber8/exe/bondype: error while loading shared libraries: libpgc.so: cannot open shared object file: No such file or directory"

Then it prints to the screen, it cannot open AM1BCC.AC files.

I searched for libpgc.so library using "find / -name libpgc.so" on my Linux system (as superuser) and could not locate it.

I'm sure this file was supplied by AMBER8...right. I am just somehow not getting access to it?

Any advice/comments would be greatly appreciated.

Thanks, Steve

> The error message is printed to the screen multiple times as:

> "The atom number exceeds the MAXATOM, reallocate memory"

Maybe this is an informational message? Have you checked the output?


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Received on Thu Mar 25 2010 - 11:00:08 PDT
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