AMBER Archive (2008)

Subject: AMBER: About reading in heme and CO molecule together with myoglobin

From: Yang, Lee-Wei (lwy1_at_pitt.edu)
Date: Mon May 05 2008 - 13:08:53 CDT

Dear Amber members,

I had technical difficulty to read in the CO molecule by tleap.

I want to study oxygenated myoglobin (In fact, CO (instead of O2) + heme + myoglobin). I get the parameters, as suggested, from frcmod.hemall and heme_all.ini available at http://amber.ch.ic.ac.uk/ff94/contrib/heme/ or installed local Amber directory. I understand the parameters may be old (although I haven't been very clear about why they are 'bad') but I should at least be able to read in all the players before I can worry about the parameters. After some hard time, I renamed all the HEME atoms in my myoglobin PDB file (1MYF-mdl1-edit.pdb) according to those defined in heme_all.in. I also realized that heme_all.in contains no topology for CO or O2 although frcmod.hemall does contain mass, bond, angle ... etc parameters for LC-LO and LO-LO. That's where causes my problem. Although HEME was read in ok, CMO (the CO) can not be properly read in, as seen in the log at http://dynamics.iam.u-tokyo.ac.jp/lee/ligated.log

LC and LO cannot be read in regardless if I change the residue name to HEM or others (such as CMO), neither can they be read in if I renumber their residue number to '2' in contrast to heme's, which is '1''.

I ran the tleap as follows:
-bash-2.05b$ tleap -s -f /home/lwy1/Mb/leaprc.ff99SB.Lee -f ./run-ligated.sh

the run-ligated.sh and all the other files I created, modified and used for this purpose are lised at http://dynamics.iam.u-tokyo.ac.jp/lee/ to await your kind examination of my ignorance.

Thank you all in advance.

Lee

ps. I left this project for a while (since last Oct, during then, I tried to have AMBER read in deoxygenated heme+proximal HIS93 + myoglobin using united atom parameter sets - leaprc.ff03ua, frcmod.hemuni and heme_uni.in and so on) and now return to have my hands back on oxygenated version. I'm still as new to Amber as last year.

Lee Wei Yang, PhD
JSPS Research Fellow,
Lab. of Molecular Design, Institute of Molecular and Cellular Biosciences,
University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
E-mail: lwy1_at_iam.u-tokyo.ac.jp Tel: +81 (0)80-3504-6690
Fax: +81-03-5841-2297
http://www.iam.u-tokyo.ac.jp/MolDes/indexE.html

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