Hi Nicolas,
You should also add the bonds to the file specbond.dat in the $GMXLIB
directory. You can search the mailing list archive for information on
this file (I believe it's not in the manual). The other thing has to
do with the bond/angletypes. Make sure you use the correct atom types
(but that's also in the specbond.dat file).
Hope it helps,
Tsjerk
On 4/20/07, martinez <[EMAIL PROTECTED]> wrote:
Hi gmx users!
I am novice in gromacs and in MD and I've been encountering a couple of
problems simulating iron sulfur clusters.
The first thing I've done is creating a new residue in the rtp files
for the 2 clusters.
Then I specified the bonds in the ffG43a1bon.itp file for my sulfur
iron bonds and modified the specbond.dat file in order to specify the
cysteine-iron bond and the histidine-iron bond. I also changed the
ffG43a1.itp file as follows
; bond-, angle- and dihedraltypes for specbonds:
[ bondtypes ]
S S 2 gb_33
NR FE 2 gb_32
; cystine - heme link (is CR1-S, use CH2-S):
S CR1 2 gb_30
; cystine - fs link:
FE S 2 gb_48
[ angletypes ]
CH1 CH2 S 2 ga_15
CH2 S S 2 ga_5
CR1 NR FE 2 ga_33
NR FE NR 2 ga_16
; cystine - heme link (is CH2-S-CR1, use CH2-S-CH2):
CH2 S CR1 2 ga_3
; cystine - heme link (is S-CR1-C/CH2, use CHn-CH2-S):
S CR1 C 2 ga_15
S CR1 CH2 2 ga_15
; cystine - fs link
S FE S 2 ga_47
FE S FE 2 ga_48
this is what pdb2gmx tells me
Special Atom Distance matrix:
CYS17 CYS20 CYS110 CYS114 CYS147 CYS187 CYS212
SG135 SG152 SG812 SG837 SG1062 SG1371 SG1570
CYS20 SG152 0.651
CYS110 SG812 1.529 1.023
CYS114 SG837 0.667 0.660 1.067
CYS147 SG1062 0.621 0.671 1.411 0.557
CYS187 SG1371 2.487 2.320 2.869 2.512 2.009
CYS212 SG1570 2.801 2.726 3.230 2.766 2.278 0.693
CYS218 SG1617 2.169 2.092 2.625 2.122 1.634 0.648 0.646
CYS227 SG1685 1.613 1.313 1.896 1.624 1.176 1.044 1.571
CYS245 SG1828 1.731 1.585 2.100 1.636 1.168 0.926 1.161
CYS248 SG1846 1.119 0.945 1.592 1.051 0.573 1.464 1.792
FS4265 FE11986 2.365 2.257 2.769 2.322 1.834 0.478 0.475
FS4265 FE21988 2.565 2.400 2.838 2.484 2.020 0.464 0.468
FS4265 FE31990 2.636 2.530 3.034 2.601 2.112 0.490 0.230
FS4265 FE41992 2.494 2.352 2.875 2.483 1.988 0.229 0.499
FS4266 FE11994 0.228 0.488 1.329 0.472 0.473 2.406 2.721
FS4266 FE21996 0.485 0.474 1.119 0.229 0.453 2.418 2.714
FS4266 FE31998 0.460 0.481 1.283 0.441 0.230 2.179 2.485
FS4266 FE42000 0.467 0.230 1.126 0.492 0.496 2.318 2.677
FS3267 FE12002 1.307 1.136 1.778 1.281 0.788 1.236 1.590
FS3267 FE22004 1.504 1.278 1.901 1.510 1.029 1.044 1.492
FS3267 FE32006 1.554 1.400 1.991 1.514 1.022 1.000 1.327
CYS218 CYS227 CYS245 CYS248 FS4265 FS4265 FS4265
SG1617 SG1685 SG1828 SG1846 FE11986 FE21988 FE31990
CYS227 SG1685 1.037
CYS245 SG1828 0.530 0.650
CYS248 SG1846 1.151 0.640 0.648
FS4265 FE11986 0.230 1.111 0.696 1.326
FS4265 FE21988 0.481 1.200 0.853 1.487 0.278
FS4265 FE31990 0.491 1.348 0.975 1.604 0.280 0.273
FS4265 FE41992 0.480 1.118 0.857 1.454 0.273 0.270 0.277
FS4266 FE11994 2.080 1.501 1.614 0.985 2.275 2.460 2.550
FS4266 FE21996 2.068 1.501 1.580 0.958 2.263 2.431 2.542
FS4266 FE31998 1.840 1.284 1.362 0.734 2.034 2.212 2.312
FS4266 FE42000 2.036 1.355 1.540 0.893 2.216 2.378 2.492
FS3267 FE12002 0.960 0.473 0.471 0.230 1.121 1.283 1.396
FS3267 FE22004 0.906 0.230 0.477 0.473 1.022 1.154 1.281
FS3267 FE32006 0.701 0.483 0.230 0.477 0.857 1.021 1.132
FS4265 FS4266 FS4266 FS4266 FS4266 FS3267 FS3267
FE41992 FE11994 FE21996 FE31998 FE42000 FE12002 FE22004
FS4266 FE11994 2.408
FS4266 FE21996 2.408 0.266
FS4266 FE31998 2.173 0.269 0.265
FS4266 FE42000 2.333 0.272 0.275 0.277
FS3267 FE12002 1.233 1.192 1.183 0.950 1.101
FS3267 FE22004 1.080 1.395 1.397 1.167 1.281 0.267
FS3267 FE32006 0.977 1.444 1.431 1.201 1.364 0.265 0.273
Linking CYS-17 SG-135 and FS4-266 FE1-1994...
Linking CYS-20 SG-152 and FS4-266 FE4-2000...
Linking CYS-114 SG-837 and FS4-266 FE2-1996...
Linking CYS-147 SG-1062 and FS4-266 FE3-1998...
Linking CYS-187 SG-1371 and FS4-265 FE4-1992...
Linking CYS-212 SG-1570 and FS4-265 FE3-1990...
Linking CYS-218 SG-1617 and FS4-265 FE1-1986...
Linking CYS-227 SG-1685 and FS3-267 FE2-2004...
Linking CYS-245 SG-1828 and FS3-267 FE3-2006...
Linking CYS-248 SG-1846 and FS3-267 FE1-2002...
N-terminus: NH3+
I have 2 questions:
Why aren't the histidines in the matrix? I think that the program
protonates first the histidines before generating the matrix with the
distances, but I'm not sure...
When I take a look at my topology file, in the[ bonds ] section, this
is what I see
2016 2017 2 gb_30
2017 2490 2
2018 2019 2 gb_4
where atom 2490 is an iron and atom 2017 is a sulfur atom from a
cysteine. Why doesn't pdb2gmx specify the bond type? It's really
strange because pdb2gmx does not give me a message error or a warning
of any kind.
Thank you for your help.
Nicolas
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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