command:<br><br>+ pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro<br>+ pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb<br>+ editconf -f a6.gro -o a6.gro -d 20.0<br>+ make_ndx -f a.pdb -o a6.ndx<br>+ grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr<br>
<br>b.pdb<br>ATOM 1 N ASP A 1 28.426 2.813 59.411 1.00 0.00<br>ATOM 2 H1 ASP A 1 28.859 2.855 58.506 1.00 0.00<br>ATOM 3 H2 ASP A 1 28.602 1.924 59.830 1.00 0.00<br>
ATOM 4 H3 ASP A 1 27.442 2.955 59.311 1.00 0.00<br>ATOM 5 CA ASP A 1 29.001 3.889 60.238 1.00 0.00<br>ATOM 6 CB ASP A 1 28.955 5.207 59.459 1.00 0.00<br>ATOM 7 CG ASP A 1 29.874 5.091 58.246 1.00 0.00<br>
ATOM 8 OD1 ASP A 1 31.097 5.071 58.485 1.00 0.00<br>ATOM 9 OD2 ASP A 1 29.330 4.852 57.149 1.00 0.00<br>ATOM 10 C ASP A 1 28.277 4.018 61.583 1.00 0.00<br>ATOM 11 O ASP A 1 27.347 3.256 61.840 1.00 0.00<br>
ATOM 12 N LYS A 2 28.790 4.934 62.412 1.00 0.00<br>ATOM 13 H LYS A 2 29.597 5.456 62.136 1.00 0.00<br>ATOM 14 CA LYS A 2 28.307 5.310 63.762 1.00 0.00<br>ATOM 15 CB LYS A 2 28.833 6.730 64.022 1.00 0.00<br>
ATOM 16 CG LYS A 2 28.551 7.291 65.418 1.00 0.00<br>ATOM 17 CD LYS A 2 29.226 8.655 65.596 1.00 0.00<br>ATOM 18 CE LYS A 2 28.832 9.371 66.894 1.00 0.00<br>ATOM 19 NZ LYS A 2 29.309 8.719 68.125 1.00 0.00<br>
ATOM 20 HZ1 LYS A 2 28.982 9.234 68.921 1.00 0.00<br>ATOM 21 HZ2 LYS A 2 28.970 7.776 68.181 1.00 0.00<br>ATOM 22 HZ3 LYS A 2 30.307 8.696 68.138 1.00 0.00<br>ATOM 23 C LYS A 2 26.773 5.209 63.930 1.00 0.00<br>
ATOM 24 O LYS A 2 26.050 5.941 63.252 1.00 0.00<br><br><br>Top file:<br>; <br>; File 'a6.top' was generated <br>
; By user: shiyong (536) <br>; On host: <a href="http://reco.bioinformatics.ku.edu">reco.bioinformatics.ku.edu</a> <br>
; At date: Mon Feb 2 18:00:37 2009 <br>; <br>; This is your topology file <br>
; "Ease Myself Into the Body Bag" (P.J. Harvey)<br>;<br>; Include forcefield parameters<br>#include "ffG53a6.itp"<br><br>; Include chain topologies<br>#include "a6_A.itp"<br>#include "a6_B.itp"<br>
#include "a6_C.itp"<br><br>; Include water topology<br>#include "spc.itp"<br><br>#ifdef POSRES_WATER<br>; Position restraint for each water oxygen<br>[ position_restraints ]<br>; i funct fcx fcy fcz<br>
1 1 1000 1000 1000<br>#endif<br><br>; Include generic topology for ions<br>#include "ions.itp"<br><br>[ system ]<br>; Name<br>Protein<br><br>[ molecules ]<br>; Compound #mols<br>Protein_A 1<br>
Protein_B 1<br>Protein_C 1<br><br><br>"atoms" section:<br><br>Protein_A 3<br><br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br>
1 NL 1 ASP N 1 0.129 14.0067 ; qtot 0.129<br> 2 H 1 ASP H1 1 0.248 1.008 ; qtot 0.377<br> 3 H 1 ASP H2 1 0.248 1.008 ; qtot 0.625<br>
4 H 1 ASP H3 1 0.248 1.008 ; qtot 0.873<br> 5 CH1 1 ASP CA 1 0.127 13.019 ; qtot 1<br> 6 CH2 1 ASP CB 2 0 14.027 ; qtot 1<br>
7 C 1 ASP CG 3 0.27 12.011 ; qtot 1.27<br> 8 OM 1 ASP OD1 3 -0.635 15.9994 ; qtot 0.635<br> 9 OM 1 ASP OD2 3 -0.635 15.9994 ; qtot 0<br>
10 C 1 ASP C 4 0.45 12.011 ; qtot 0.45<br> 11 O 1 ASP O 4 -0.45 15.9994 ; qtot 0<br> 12 N 2 LYSH N 5 -0.31 14.0067 ; qtot -0.31<br>
13 H 2 LYSH H 5 0.31 1.008 ; qtot 0<br> 14 CH1 2 LYSH CA 6 0 13.019 ; qtot 0<br> 15 CH2 2 LYSH CB 6 0 14.027 ; qtot 0<br>
16 CH2 2 LYSH CG 7 0 14.027 ; qtot 0<br> 17 CH2 2 LYSH CD 7 0 14.027 ; qtot 0<br> 18 CH2 2 LYSH CE 8 0.127 14.027 ; qtot 0.127<br>
19 NL 2 LYSH NZ 8 0.129 14.0067 ; qtot 0.256<br> 20 H 2 LYSH HZ1 8 0.248 1.008 ; qtot 0.504<br> 21 H 2 LYSH HZ2 8 0.248 1.008 ; qtot 0.752<br>
22 H 2 LYSH HZ3 8 0.248 1.008 ; qtot 1<br> 23 C 2 LYSH C 9 0.45 12.011 ; qtot 1.45<br> 24 O 2 LYSH O 9 -0.45 15.9994 ; qtot 1<br>
<br><br>index groups<br><br>[ chAANDB_&_!H* ]<br> 1 5 6 7 8 9 10 11 12 14 15 16 17 18 19<br> 23 24 25 26 27 28 29 30 31 32 34 35 36 37 38<br> 39 40 41 43 44 45 46 48 49 51 52 54 56 58 60<br>
61 62 64 65 66 67 68 69 70 71 72 74 75 76 77<br>....<br>2569 2570<br><br>[ chC_&_!H* ]<br>2571 2575 2576 2577 2578 2580 2581 2582 2583 2584 2585 2586 2587 2588 2589<br>2590 2591 2592 2593 2594 2595 2597 2598 2599 2600 2601 2602 2605 2606 2607<br>
....<br><br> <br><br><br><div class="gmail_quote">On Mon, Feb 2, 2009 at 5:46 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="Ih2E3d"><br>
<br>
Liu Shiyong wrote:<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Here is my command.<br>
<br>
pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o<br>
a6.gro<br>
<br>
pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb<br>
<br>
<br>
Why are you running pdb2gmx twice? Unless you have multiple<br>
proteins, and need multiple topologies, you should not be doing this.<br>
<br>
<br>
<br>
That's because the *.gro file does not include chain id information.<br>
<br>
If I run make_ndx -f a6.gro -o a6.ndx<br>
<br>
I will get :<br>
<br>
Found 0 atoms with chain identifiers A AND B<br>
><br>
Found 0 atoms with chain identifier C<br>
<br>
</blockquote>
<br></div>
Alright, I was just confused why you're running pdb2gmx twice to get the desired output. If you need a .pdb file, then just choose it as your output format the first time you run the command. I would recommend not dealing with multiple iterations of the same command; it can lead to confusion.<div class="Ih2E3d">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
editconf -f a6.gro -o a6.gro -d 20.0<br>
<br>
<br>
You realize that the units of -d are nm, right? Do you need such a<br>
huge solute-box distance?<br>
<br>
I know the units is nm.<br>
</blockquote>
<br></div>
Just checking :)<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
</blockquote>
<br>
<snip><div class="Ih2E3d"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
-------------------------------------------------------<br>
Program grompp, VERSION 4.0.2<br>
Source code file: grompp.c, line: 150<br>
Fatal error:<br>
atoms 1 and 2 in charge group 1 of molecule type<br>
'Protein_A' are<br>
in different energy groups<br>
-------------------------------------------------------<br>
</blockquote>
<br></div>
There is still some sort of disconnect between topology numbering (which is where charge groups are defined), and the structure you are using. Can you post the first *few* lines of your .pdb file, [ atoms ] section of the .top, and the relevant index groups?<br>
<font color="#888888">
<br>
-Justin</font><div><div></div><div class="Wj3C7c"><br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (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>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Shiyong Liu<br>Postdoc<br>center for bioinformatics in the university of kansas<br>Lab: (785)864-1962<br>Email: <a href="mailto:syliu@ku.edu">syliu@ku.edu</a> (<a href="mailto:shiyongliu@ku.edu">shiyongliu@ku.edu</a> or <a href="mailto:liushiyong@ku.edu">liushiyong@ku.edu</a>)<br>
Homepage: <a href="http://www.people.ku.edu/~syliu">http://www.people.ku.edu/~syliu</a><br>Lab: <a href="http://vakser.bioinformatics.ku.edu/people">http://vakser.bioinformatics.ku.edu/people</a><br>Phone:         (785) 864-1962<br>