<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial,helvetica,sans-serif;font-size:12pt">dear Justin<br><div>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?)<br>all the best<br>sajad<br><br><span style="background-color: rgb(0, 127, 64);">topology for ADP:</span><br><pre>0 0 2<br><br>R-ADENOSINE - with diphosphate linker<br>adp.db94<br> adp INT 1<br> CORRECT OMIT DU BEG<br> 0.0<br> 1 DUMM DU M 0 0 0 0.000 0.000 0.000 0.000<br> 2 DUMM DU M 1 0 0 1.000 0.000 0.000 0.000<br> 3 DUMM DU M 2 1 0 1.000
90.000 0.000 0.000<br> 4 O1B O3 M 3 2 1 1.000 90.000 180.000 -0.9552<br> 5 PB P M 4 3 2 1.434 90.000 180.000 1.3672<br> 6 O2B O3 E 5 4 3 1.574 107.490 -79.441 -0.9552<br> 7 O3B O3 E 5 4 3 1.518 118.007 165.990 -0.9552<br> 8 O3A OS M 5 4 3 1.599 113.374 180.000 -0.6346<br> 9 PA P M 6 5 4 1.646 130.619 36.624 1.4929<br> 10 O1A O2 E 7 6 5 1.504 109.212 -90.234 -0.9474<br> 11 O2A O2 E 7 6 5 1.526 108.570 40.323 -0.9474<br> 12 O5* OS M 7 6 5 1.585 97.173 157.726 -0.6579<br> 13 C5* CT M 8 7 6 1.445 122.292 -66.317 0.0558<br> 14 H50 H1 E 9 8 7 1.059 109.484 27.531 0.0679<br> 15 H51 H1 E 9 8 7 1.059 109.437 -92.456 0.0679<br>
16 C4* CT M 9 8 7 1.477 113.286 147.538 0.1065<br> 17 H40 H1 E 16 9 8 1.059 105.768 -179.178 0.1174<br> 18 O4* OS S 16 13 9 1.482 106.235 -62.889 -0.3548<br> 19 C1* CT B 18 16 13 1.391 107.688 128.804 0.0394<br> 20 H10 H2 E 19 18 16 1.059 109.468 91.228 0.2007<br> 21 N9 N* S 19 18 16 1.552 105.091 -143.300 -0.0251<br> 22 C8 CK B 21 19 18 1.388 123.797 33.434 0.2006<br> 23 H80 H5 E 22 21 19 1.078 131.047 -3.389 0.1553<br> 24 N7 NB S 22 21 19 1.384 108.967 176.598 -0.6073<br> 25 C5 CB S 24 22 21 1.395 103.021 0.702 0.0515<br> 26 C6 CA B 25 24 22 1.412 128.288 178.252 0.7009<br> 27 N6 N2 B 26 25 24 1.333 125.907 -3.791 -0.9019<br> 28 H60 H E 27 26
25 1.010 120.010 2.829 0.4115<br> 29 H61 H E 27 26 25 1.009 120.014 -177.167 0.4115<br> 30 N1 NC S 26 25 24 1.343 113.319 178.851 -0.7615<br> 31 C2 CQ B 30 26 25 1.340 123.433 -1.664 0.5875<br> 32 H2 H5 E 31 30 26 1.077 120.022 -177.875 0.0473<br> 33 N3 NC S 31 30 26 1.377 125.379 2.123 -0.6997<br> 34 C4 CB E 33 31 30 1.300 108.242 -0.035 0.3053<br> 35 C3* CT M 16 13 12 1.484 117.051 57.581 0.2022<br> 36 H30 H1 E 35 16 13 1.059 117.939 24.820 0.0615<br> 37 O3* OH S 35 16 13 1.407 108.509 149.908 -0.6541<br> 38 H3* HO E 37 35 16 0.967 109.470 163.254 0.4376<br> 39 C2* CT M 35 16 13 1.607 102.425 -96.715 0.0670<br> 40 H20 H1 E 39 35 16 1.059 115.086 78.119
0.0972<br> 41 O2* OH S 39 35 16 1.398 114.943 -153.294 -0.6139<br> 42 H2* HO E 41 39 35 0.967 109.456 -41.679 0.4186<br><br>IMPROPER<br> C8 C4 N9 C1*<br> C6 H60 N6 H61<br> N7 N9 C8 H80<br> N1 N3 C2 H2<br><br><br><span style="background-color: rgb(0, 191, 96);">topology for ATP:</span><br><br>0 0 2<br><br>R-ADENOSINE - with triphosphate linker<br>atp.db94<br> atp INT 1<br> CORRECT OMIT DU BEG<br> 0.0<br> 1 DUMM DU M 0 0 0 1.000 90.000 180.000 0.000<br> 2 DUMM DU M 1 0 0 0.967 90.000 180.000 0.000<br> 3 DUMM DU M 2 1 0 0.967 109.443 180.000 0.000<br> 4 O1G O3 M 3 2 1 1.086 160.811 148.238 -0.9526<br> 5 PG P M 4 3 2 1.379 92.848 -159.681 1.2650<br> 6 O2G O3 E 5 4 3 1.417 116.381 -173.072 -0.9526<br> 7 O3G
O3 E 5 4 3 1.443 104.744 40.954 -0.9526<br> 8 O3B OS M 5 4 3 1.742 94.444 -63.733 -0.5322<br> 9 PB P M 8 5 3 1.512 135.464 -125.176 1.3852<br> 10 O1B O2 E 9 8 5 1.415 113.542 -28.935 -0.8894<br> 11 O2B O2 E 9 8 5 1.617 103.881 -164.747 -0.8894<br> 12 O3A OS M 9 8 5 1.734 96.237 83.499 -0.5689<br> 13 PA P M 12 9 8 1.516 131.613 -127.461 1.2532<br> 14 O1A O2 E 13 12 9 1.526 115.352 -92.892 -0.8799<br> 15 O2A O2 E 13 12 9 1.410 109.213 53.806 -0.8799<br> 16 O5* OS M 13 12 9 1.749 97.280 164.349 -0.5987<br> 17 C5* CT M 16 13 12 1.427 117.355 64.264 0.0558<br> 18 H50 H1 E 17 16 13 1.059 109.461 103.970 0.0679<br> 19 H51 H1 E 17 16 13
1.059 109.491 -16.065 0.0679<br> 20 C4* CT M 17 16 13 1.446 107.888 -136.043 0.1065<br> 21 H40 H1 E 20 17 16 1.059 106.572 -167.965 0.1174<br> 22 O4* OS S 20 17 16 1.577 105.136 -48.024 -0.3548<br> 23 C1* CT B 22 20 17 1.562 99.310 148.198 0.0394<br> 24 H10 H2 E 23 22 20 1.059 104.667 127.006 0.2007<br> 25 N9 N* S 23 22 20 1.651 99.707 -129.444 -0.0251<br> 26 C8 CK B 25 23 22 1.400 121.683 69.274 0.2006<br> 27 H80 H5 E 26 25 23 1.077 128.168 2.532 0.1553<br> 28 N7 NB S 26 25 23 1.327 111.806 -177.463 -0.6073<br> 29 C5 CB S 28 26 25 1.365 104.681 2.256 0.0515<br> 30 C6 CA B 29 28 26 1.448 131.894 -177.019 0.7009<br> 31 N6 N2 B 30 29 28 1.312 123.747 -3.485
-0.9019<br> 32 H60 H E 31 30 29 1.000 120.000 176.690 0.4115<br> 33 H61 H E 31 30 29 1.000 120.000 -3.310 0.4115<br> 34 N1 NC S 30 29 28 1.362 114.694 173.408 -0.7615<br> 35 C2 CQ B 34 30 29 1.370 122.869 5.034 0.5875<br> 36 H2 H5 E 35 34 30 1.078 119.995 174.203 0.0473<br> 37 N3 NC S 35 34 30 1.309 125.548 -5.799 -0.6997<br> 38 C4 CB E 37 35 34 1.340 112.610 1.051 0.3053<br> 39 C3* CT M 20 17 16 1.539 120.245 66.848 0.2022<br> 40 H30 H1 E 39 20 17 1.059 109.025 -37.638 0.0615<br> 41 O3* OH S 39 20 17 1.390 114.084 86.172 -0.6541<br> 42 H3' HO E 41 39 20 0.967 109.487 -2.526 0.4376<br> 43 C2* CT M 39 20 17 1.606 106.034 -155.382 0.0670<br> 44 H20 H1
E 43 39 20 1.059 123.901 158.202 0.0972<br> 45 O2* OH S 43 39 20 1.368 107.234 -72.414 -0.6139<br> 46 H2' HO E 45 43 39 0.967 109.442 -16.862 0.4186<br><br>IMPROPER<br> C8 C4 N9 C1*<br> C6 H60 N6 H61<br> N7 N9 C8 H80<br> N1 N3 C2 H2<br> C5 N1 C6 N6<br><br>LOOP CLOSING EXPLICIT<br> C1* C2*<br> C4 C5<br> C4 N9<br><br>DONE<br>STOP<br><br><br></pre><br><br></div><div style="font-family: arial,helvetica,sans-serif; font-size: 12pt;"><br><div style="font-family: arial,helvetica,sans-serif; font-size: 13px;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br><b><span style="font-weight: bold;">To:</span></b> Gromacs Users' List <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Sat, April 23, 2011 5:46:24 PM<br><b><span style="font-weight:
bold;">Subject:</span></b> Re: [gmx-users] dealing with ATP<br></font><br>
<br><br>Sajad Ahrari wrote:<br>> tnx for your help Justin!<br>> 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!?<br><br>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.<br><br>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.<br><br>If you need to
simulation this ADP-SO4 species, you're in for the long road of parameterization:<br><br><span><a target="_blank" href="http://www.gromacs.org/Documentation/How-tos/Parameterization">http://www.gromacs.org/Documentation/How-tos/Parameterization</a></span><br><br>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.<br><br>-Justin<br><br>> regards<br>> sajad<br>> <br>> ------------------------------------------------------------------------<br>> *From:* Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *To:* Discussion list for GROMACS users <<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>>
*Sent:* Sat, April 23, 2011 5:54:58 AM<br>> *Subject:* Re: [gmx-users] dealing with ATP<br>> <br>> <br>> <br>> Sajad Ahrari wrote:<br>> > Dear users<br>> > 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<br>> <br>> No, but you can use a text editor to replace the S atom with P.<br>> <br>> > i need to introduce ATP for Gromacs or it is known for the program?<br>> <br>> Some force fields support ATP, some do not. Check the .rtp files and see what you find.<br>> <br>> -Justin<br>> <br>> > i do appreciate your help!<br>> > sajad<br>> ><br>> <br>> -- ========================================<br>>
<br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]<a target="_blank" href="http://vt.edu">vt.edu</a><span> <<a target="_blank" href="http://vt.edu/">http://vt.edu/</a>> | (540) 231-9080</span><br><span>> <a target="_blank" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></span><br>> <br>> ========================================<br>> -- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br><span>> <a target="_blank"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span><br><span>> Please search the archive at <a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!</span><br>> Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> <mailto:<a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br><span>> Can't post? Read <a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a></span><br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral
Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]vt.edu | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a ymailto="mailto:gmx-users-request@gromacs.org"
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