AMBER: Antechamber functionality, MOL2 files

From: bigbrainstorm <>
Date: Tue, 12 Aug 2003 19:50:40 -0700

Dear AMBER community,

    I am using Amber 7 on Linux and O2 SGI machines. I am attempting to simulate a system consisting of two separate but catenated organic molecules. My starting structure is a MOL2 file. I am using babel to convert this into a pdb file and load that into XLEAP for positional coordinates. I am having some difficulty generating prep files. Unfortunately, I can't seem to get Antechamber to read both molecules simultaneously, and I can't split the MOL2 file into two separate files because the atomic numbering scheme in the MOL2 seems to "mix" both molecules together, and there is no single point of division. The whole system is on the order of >450 heavy atoms, so I would really prefer to avoid hand editing.
    Is there any way that Antwechamber could be used to generate a single prep file out of two molecules in a single file? Alternatively, does anyone know of a program that would allow me to renumber the MOL2 file so that I could split it up manually?
I would appreciate any help you could give me.

Yours Truly,

Zeve Akerling, UCLA, Undergraduate Summer Research Program.
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Aug 13 2003 - 04:53:01 PDT
Custom Search