Message: 6
Date: Tue, 25 Nov 2008 07:17:14 -0500
From: "Justin A. Lemkul" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Loss of bonds in HEME iron after pdb2gmx
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
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[EMAIL PROTECTED] wrote:
Hello,
Sorry, I realised the HEME HEC naming was not the problem. But still the
pdb2gmx causes loss of all bonds of FE in HEME. The cystine also gets
protonated and doesnot form a bond with HEME. I tried to preserve the
bonds by editing the specbond.dat file. I do not know if it can be used
for intramolecular bonding. Kindly inform if the modifications I have
made
are valid. The runtime information during the execution of pdb2gmx
indicated the linking of FE in HEME to the N atoms. However, I do not
see
the bonds when I open the output file in Pymol. Please indicate how this
problem can be resolved.
Well, using visualization software may not indicate anything. Most
programs
decide on bonds based on distance, not any sort of intelligent mechanism.
The
question is whether or not these bonds show up in your topol.top.
This is the content of my specbond.dat file:
5
CYS SG 1 HEME FE 5 0.25 CYS HEME
Well, this may be why your Cys is getting protonated - you're telling
pdb2gmx
that it should be! See the format of specbond.dat here:
http://wiki.gromacs.org/index.php/specbond.dat
The second-to-last column should be the new residue name for cysteine,
probably
you want something like CYS2.
HEME FE 5 HEME NA 3 0.22 HEME HEME
HEME FE 5 HEME NB 3 0.22 HEME HEME
HEME FE 5 HEME NC 3 0.22 HEME HEME
HEME FE 5 HEME ND 3 0.22 HEME HEME
Why is this section (above) even necessary? Are these bonds not defined
in the
.rtp file of your force field? Which force field are you using? I know
these
are defined in the Gromos-type force fields.
Try again with the original specbond.dat, but don't assume that
visualization
software will always indicate the presence/absence of a bond. Examine
your
topology for that.
-Justin
And these I obtained during the execution of pdbgmx:
Opening library file specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
Special Atom Distance matrix:
CYS122 CYS135 CYS143 CYS146 CYS150 CYS237 CYS309
SG958 SG1059 SG1118 SG1136 SG1165 SG1902 SG2475
CYS135 SG1059 1.677
CYS143 SG1118 1.076 1.092
CYS146 SG1136 1.313 1.792 0.749
CYS150 SG1165 1.175 2.054 0.978 0.426
CYS237 SG1902 2.194 3.510 2.536 1.933 1.632
CYS309 SG2475 1.745 2.703 2.469 2.507 2.423 2.449
CYS343 SG2748 4.679 4.998 4.364 3.763 3.870 3.329 4.426
CYS406 SG3265 2.258 2.657 2.051 1.603 1.744 1.886 2.198
CYS457 SG3657 2.232 0.829 1.894 2.582 2.825 4.173 2.898
HEME462 FE3693 2.257 2.566 1.949 1.489 1.669 1.956 2.343
HEME462 NA3694 2.456 2.680 2.110 1.663 1.862 2.118 2.486
HEME462 NB3695 2.199 2.426 1.883 1.498 1.704 2.088 2.247
HEME462 NC3696 2.061 2.462 1.795 1.321 1.479 1.809 2.217
HEME462 ND3697 2.331 2.711 2.031 1.505 1.657 1.841 2.455
CYS343 CYS406 CYS457 HEME462 HEME462 HEME462 HEME462
SG2748 SG3265 SG3657 FE3693 NA3694 NB3695 NC3696
CYS406 SG3265 2.501
CYS457 SG3657 5.547 3.210
HEME462 FE3693 2.512 0.219 3.147
HEME462 NA3694 2.361 0.325 3.240 0.211
HEME462 NB3695 2.647 0.293 2.977 0.208 0.295
HEME462 NC3696 2.671 0.286 3.064 0.209 0.420 0.297
HEME462 ND3697 2.389 0.314 3.318 0.208 0.297 0.416 0.293
Linking HEME-462 FE-3693 and HEME-462 NA-3694...
Linking HEME-462 FE-3693 and HEME-462 NB-3695...
Linking HEME-462 FE-3693 and HEME-462 NC-3696...
Linking HEME-462 FE-3693 and HEME-462 ND-3697...
N-terminus: PRO-NH2+
C-terminus: COO-
Now there are 462 residues with 4749 atoms
Making bonds...
Thanks.
Sarada
Graduate Student,
NCBS, Bangalore
Hello,
I am working with the simulation of cytochromeP450. In the output of the
pdb2gmx command, the iron atom in the HEME loses all the bonds,
including
the sulphide bond with cystine. Also, the command changed the residue
name
from HEME to HEC. During the execution of the pdb2gmx, I get this
warning:
Warning: 'HEC' not found in residue topology database, trying to use
'HEME'
Can someone please tell me, if this is responsible for the loss of bonds
especially the one between CYS and FE. How can the bonds be retained?
Thanks.
Sarada
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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