On 4/25/2011 8:05 PM, Sajad Ahrari wrote:
dear Justin
it seems that, ADP and ATP are not known to any of gromacs
forcefields. but their topologies have been described in amber web
site(as follows). should i be adding them to .tpr file of gromacs? if
so, how can i access this file and is there any modification being
needed in what amber has introduced? (or i have to just do something
like copy and paste?)
This is doable, but there's probably no automatic conversion software,
because nobody's needed to do this so often that writing software was
worthwhile. So you'll have to spend some time with the AMBER and GROMACS
documentation, to learn how to do the conversion of the parameters and
functions between different file formats.
Mark
all the best
sajad
topology for ADP:
0 0 2
R-ADENOSINE - with diphosphate linker
adp.db94
adp INT 1
CORRECT OMIT DU BEG
0.0
1 DUMM DU M 0 0 0 0.000 0.000 0.000 0.000
2 DUMM DU M 1 0 0 1.000 0.000 0.000 0.000
3 DUMM DU M 2 1 0 1.000
90.000 0.000 0.000
4 O1B O3 M 3 2 1 1.000 90.000 180.000 -0.9552
5 PB P M 4 3 2 1.434 90.000 180.000 1.3672
6 O2B O3 E 5 4 3 1.574 107.490 -79.441 -0.9552
7 O3B O3 E 5 4 3 1.518 118.007 165.990 -0.9552
8 O3A OS M 5 4 3 1.599 113.374 180.000 -0.6346
9 PA P M 6 5 4 1.646 130.619 36.624 1.4929
10 O1A O2 E 7 6 5 1.504 109.212 -90.234 -0.9474
11 O2A O2 E 7 6 5 1.526 108.570 40.323 -0.9474
12 O5* OS M 7 6 5 1.585 97.173 157.726 -0.6579
13 C5* CT M 8 7 6 1.445 122.292 -66.317 0.0558
14 H50 H1 E 9 8 7 1.059 109.484 27.531 0.0679
15 H51 H1 E 9 8 7 1.059 109.437 -92.456 0.0679
16 C4* CT M 9 8 7 1.477 113.286 147.538 0.1065
17 H40 H1 E 16 9 8 1.059 105.768 -179.178 0.1174
18 O4* OS S 16 13 9 1.482 106.235 -62.889 -0.3548
19 C1* CT B 18 16 13 1.391 107.688 128.804 0.0394
20 H10 H2 E 19 18 16 1.059 109.468 91.228 0.2007
21 N9 N* S 19 18 16 1.552 105.091 -143.300 -0.0251
22 C8 CK B 21 19 18 1.388 123.797 33.434 0.2006
23 H80 H5 E 22 21 19 1.078 131.047 -3.389 0.1553
24 N7 NB S 22 21 19 1.384 108.967 176.598 -0.6073
25 C5 CB S 24 22 21 1.395 103.021 0.702 0.0515
26 C6 CA B 25 24 22 1.412 128.288 178.252 0.7009
27 N6 N2 B 26 25 24 1.333 125.907 -3.791 -0.9019
28 H60 H E 27 26
25 1.010 120.010 2.829 0.4115
29 H61 H E 27 26 25 1.009 120.014 -177.167 0.4115
30 N1 NC S 26 25 24 1.343 113.319 178.851 -0.7615
31 C2 CQ B 30 26 25 1.340 123.433 -1.664 0.5875
32 H2 H5 E 31 30 26 1.077 120.022 -177.875 0.0473
33 N3 NC S 31 30 26 1.377 125.379 2.123 -0.6997
34 C4 CB E 33 31 30 1.300 108.242 -0.035 0.3053
35 C3* CT M 16 13 12 1.484 117.051 57.581 0.2022
36 H30 H1 E 35 16 13 1.059 117.939 24.820 0.0615
37 O3* OH S 35 16 13 1.407 108.509 149.908 -0.6541
38 H3* HO E 37 35 16 0.967 109.470 163.254 0.4376
39 C2* CT M 35 16 13 1.607 102.425 -96.715 0.0670
40 H20 H1 E 39 35 16 1.059 115.086 78.119
0.0972
41 O2* OH S 39 35 16 1.398 114.943 -153.294 -0.6139
42 H2* HO E 41 39 35 0.967 109.456 -41.679 0.4186
IMPROPER
C8 C4 N9 C1*
C6 H60 N6 H61
N7 N9 C8 H80
N1 N3 C2 H2
topology for ATP:
0 0 2
R-ADENOSINE - with triphosphate linker
atp.db94
atp INT 1
CORRECT OMIT DU BEG
0.0
1 DUMM DU M 0 0 0 1.000 90.000 180.000 0.000
2 DUMM DU M 1 0 0 0.967 90.000 180.000 0.000
3 DUMM DU M 2 1 0 0.967 109.443 180.000 0.000
4 O1G O3 M 3 2 1 1.086 160.811 148.238 -0.9526
5 PG P M 4 3 2 1.379 92.848 -159.681 1.2650
6 O2G O3 E 5 4 3 1.417 116.381 -173.072 -0.9526
7 O3G
O3 E 5 4 3 1.443 104.744 40.954 -0.9526
8 O3B OS M 5 4 3 1.742 94.444 -63.733 -0.5322
9 PB P M 8 5 3 1.512 135.464 -125.176 1.3852
10 O1B O2 E 9 8 5 1.415 113.542 -28.935 -0.8894
11 O2B O2 E 9 8 5 1.617 103.881 -164.747 -0.8894
12 O3A OS M 9 8 5 1.734 96.237 83.499 -0.5689
13 PA P M 12 9 8 1.516 131.613 -127.461 1.2532
14 O1A O2 E 13 12 9 1.526 115.352 -92.892 -0.8799
15 O2A O2 E 13 12 9 1.410 109.213 53.806 -0.8799
16 O5* OS M 13 12 9 1.749 97.280 164.349 -0.5987
17 C5* CT M 16 13 12 1.427 117.355 64.264 0.0558
18 H50 H1 E 17 16 13 1.059 109.461 103.970 0.0679
19 H51 H1 E 17 16 13
1.059 109.491 -16.065 0.0679
20 C4* CT M 17 16 13 1.446 107.888 -136.043 0.1065
21 H40 H1 E 20 17 16 1.059 106.572 -167.965 0.1174
22 O4* OS S 20 17 16 1.577 105.136 -48.024 -0.3548
23 C1* CT B 22 20 17 1.562 99.310 148.198 0.0394
24 H10 H2 E 23 22 20 1.059 104.667 127.006 0.2007
25 N9 N* S 23 22 20 1.651 99.707 -129.444 -0.0251
26 C8 CK B 25 23 22 1.400 121.683 69.274 0.2006
27 H80 H5 E 26 25 23 1.077 128.168 2.532 0.1553
28 N7 NB S 26 25 23 1.327 111.806 -177.463 -0.6073
29 C5 CB S 28 26 25 1.365 104.681 2.256 0.0515
30 C6 CA B 29 28 26 1.448 131.894 -177.019 0.7009
31 N6 N2 B 30 29 28 1.312 123.747 -3.485
-0.9019
32 H60 H E 31 30 29 1.000 120.000 176.690 0.4115
33 H61 H E 31 30 29 1.000 120.000 -3.310 0.4115
34 N1 NC S 30 29 28 1.362 114.694 173.408 -0.7615
35 C2 CQ B 34 30 29 1.370 122.869 5.034 0.5875
36 H2 H5 E 35 34 30 1.078 119.995 174.203 0.0473
37 N3 NC S 35 34 30 1.309 125.548 -5.799 -0.6997
38 C4 CB E 37 35 34 1.340 112.610 1.051 0.3053
39 C3* CT M 20 17 16 1.539 120.245 66.848 0.2022
40 H30 H1 E 39 20 17 1.059 109.025 -37.638 0.0615
41 O3* OH S 39 20 17 1.390 114.084 86.172 -0.6541
42 H3' HO E 41 39 20 0.967 109.487 -2.526 0.4376
43 C2* CT M 39 20 17 1.606 106.034 -155.382 0.0670
44 H20 H1
E 43 39 20 1.059 123.901 158.202 0.0972
45 O2* OH S 43 39 20 1.368 107.234 -72.414 -0.6139
46 H2' HO E 45 43 39 0.967 109.442 -16.862 0.4186
IMPROPER
C8 C4 N9 C1*
C6 H60 N6 H61
N7 N9 C8 H80
N1 N3 C2 H2
C5 N1 C6 N6
LOOP CLOSING EXPLICIT
C1* C2*
C4 C5
C4 N9
DONE
STOP
------------------------------------------------------------------------
*From:* Justin A. Lemkul <jalem...@vt.edu>
*To:* Gromacs Users' List <gmx-users@gromacs.org>
*Sent:* Sat, April 23, 2011 5:46:24 PM
*Subject:* Re: [gmx-users] dealing with ATP
Sajad Ahrari wrote:
> tnx for your help Justin!
> but shouldn't the topology of S atom be described for gromacs?
unless gromacs may know P atom with the same topology as S. although
they may not be the same!?
You're talking about two separate issues - atom types and parameters
for molecules. Yes, most (all?) force fields describe both P and S
atoms, but I guarantee none of them have (by default) parameters for
some species named "d" that represents ADP-SO4. You cannot assign
parameters from P blindly to S and hope for the best. That sounds
fundamentally wrong to me.
In your original message, it sounded like you wanted to change ADP-SO4
into ATP, but perhaps I misunderstood what you intended. No force
field will be able to assign parameters to ADP-SO4, even though the
force field may recognize individual atoms, it cannot construct a
topology for any arbitrary molecules.
If you need to simulation this ADP-SO4 species, you're in for the long
road of parameterization:
http://www.gromacs.org/Documentation/How-tos/Parameterization
Otherwise, change the S atom to P and name the molecule ATP so it will
be recognized by whatever force field you choose, after you have
verified that the force field can indeed recognize such a species.
Otherwise, you're stuck doing parameterization for ATP, too.
-Justin
> regards
> sajad
>
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
> *To:* Discussion list for GROMACS users <gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
> *Sent:* Sat, April 23, 2011 5:54:58 AM
> *Subject:* Re: [gmx-users] dealing with ATP
>
>
>
> Sajad Ahrari wrote:
> > Dear users
> > i am working with a protein witch holds a hetero-atom in it's pdb
structure. the hetero-atom is named "d" and stands for "ADP+SO4" (in
fact the third phosphate of ATP is being substituted with SO4). i
wanted to know if gromacs holds a feature to change "d" into ATP? and
if so do
>
> No, but you can use a text editor to replace the S atom with P.
>
> > i need to introduce ATP for Gromacs or it is known for the program?
>
> Some force fields support ATP, some do not. Check the .rtp files
and see what you find.
>
> -Justin
>
> > i do appreciate your help!
> > sajad
> >
>
> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu><http://vt.edu/> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> -- gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
-- gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
