RE: Par and Top files for BCL

From: Kovács, Sándor Ádám (skovacs_at_wustl.edu)
Date: Thu Jul 09 2009 - 13:35:54 CDT

Good news!

After a week of some extensive trial and error methods using paratool, I stumbled across the following website which has parameter and topology files for a variety of compounds, including BCL.

http://xray.bmc.uu.se/hicup/

As with any input files, make sure to double check masses, bonds, dihedrals, etc.
Also be sure to cite the website as described on its home page.

I hope this helps some of you searching for similar files!

Sándor

-----Original Message-----
From: Kovács, Sándor Ádám
Sent: Thu 7/2/2009 12:08 PM
To: namd-l_at_ks.uiuc.edu
Subject: Par and Top files for BCL
 
Greetings,

I'm attempting to run NAMD simulations on the complete FMO trimer (PDB: 3ENI), which is part of the photosynthetic complex in many plants.
After an extensive google search, scouring of various forums, and visiting websites of groups already well-established in the area,
I have been unable to locate parameter and topology files for the bacteriochlorophyll A molecule, identified in the PDB file as "RESI BCL".

I would be grateful if anyone already has these files and is willing to share.

Meanwhile, I'll try and create ones using the parameterization tool included with VMD, and if I'm successful, I'll post it for others.

Thanks!
Sándor

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