[AMBER] Chlorophyll A .mol2 file

From: Ofir Tal <pantufel.hotmail.com>
Date: Thu, 2 Jul 2015 13:45:12 +0000

Dear Amber members,

We are facing a major problem with constructing a .mol2 file of ChlorophyllA-Mg2+ molecule with PS-I complex in a membrane.

ANTECHAMBER doesn't know how to do it due to 'Open shell' in the ChlA molecule. We tried to use RED for creating .mol2 but either the job is killed (producing no results) or the output .mol2 file is wrong (metal coordinations are wrong, atoms connectivity is wrong, ect...). When trying to do a test minimization with AMBER, after producing such a RED mol2 file, the system is killed with errors like below:
forrtl: severe (174): SIGSEGV, segmentation fault occurred

When doing it without the Chlorophyll+MG complex, the system works great (but there are > 70 ChlA molecules which are relevant).

There are few old posts regarding the ChlA problem but no reproducible solution was raised.
I would very appreciate your help with it. If anyone can direct us to the solution, a protocol, or even a correct [Chlorophyll A - Mg2+] .mol2 files to be shared.

Thank you!

All the best,

Ofir Tal, PhD
Structural Bioinformatics
Bioinformatics Knowledge Unit - BKU

The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of TechnologyHaifa 32000, ISRAEL
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Received on Thu Jul 02 2015 - 07:00:04 PDT
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