[gmx-users] Problems with pdb2gmx simulating a iron-sulfur cluster
Tsjerk Wassenaar
tsjerkw at gmail.com
Fri Apr 20 18:04:53 CEST 2007
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 <nicolas.martinez at ibs.fr> 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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