[gmx-users] energy groups
Justin A. Lemkul
jalemkul at vt.edu
Tue Feb 3 01:35:49 CET 2009
Alright, none of this looks like it will cause a problem. Can you post your
em.mdp file?
-Justin
Liu Shiyong wrote:
> command:
>
> + pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o a6.gro
> + pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb
> + editconf -f a6.gro -o a6.gro -d 20.0
> + make_ndx -f a.pdb -o a6.ndx
> + grompp -maxwarn 10 -f em.mdp -c a6.gro -n a6.ndx -p a6.top -o a6.input.tpr
>
> b.pdb
> ATOM 1 N ASP A 1 28.426 2.813 59.411 1.00 0.00
> ATOM 2 H1 ASP A 1 28.859 2.855 58.506 1.00 0.00
> ATOM 3 H2 ASP A 1 28.602 1.924 59.830 1.00 0.00
> ATOM 4 H3 ASP A 1 27.442 2.955 59.311 1.00 0.00
> ATOM 5 CA ASP A 1 29.001 3.889 60.238 1.00 0.00
> ATOM 6 CB ASP A 1 28.955 5.207 59.459 1.00 0.00
> ATOM 7 CG ASP A 1 29.874 5.091 58.246 1.00 0.00
> ATOM 8 OD1 ASP A 1 31.097 5.071 58.485 1.00 0.00
> ATOM 9 OD2 ASP A 1 29.330 4.852 57.149 1.00 0.00
> ATOM 10 C ASP A 1 28.277 4.018 61.583 1.00 0.00
> ATOM 11 O ASP A 1 27.347 3.256 61.840 1.00 0.00
> ATOM 12 N LYS A 2 28.790 4.934 62.412 1.00 0.00
> ATOM 13 H LYS A 2 29.597 5.456 62.136 1.00 0.00
> ATOM 14 CA LYS A 2 28.307 5.310 63.762 1.00 0.00
> ATOM 15 CB LYS A 2 28.833 6.730 64.022 1.00 0.00
> ATOM 16 CG LYS A 2 28.551 7.291 65.418 1.00 0.00
> ATOM 17 CD LYS A 2 29.226 8.655 65.596 1.00 0.00
> ATOM 18 CE LYS A 2 28.832 9.371 66.894 1.00 0.00
> ATOM 19 NZ LYS A 2 29.309 8.719 68.125 1.00 0.00
> ATOM 20 HZ1 LYS A 2 28.982 9.234 68.921 1.00 0.00
> ATOM 21 HZ2 LYS A 2 28.970 7.776 68.181 1.00 0.00
> ATOM 22 HZ3 LYS A 2 30.307 8.696 68.138 1.00 0.00
> ATOM 23 C LYS A 2 26.773 5.209 63.930 1.00 0.00
> ATOM 24 O LYS A 2 26.050 5.941 63.252 1.00 0.00
>
>
> Top file:
> ;
>
> ; File 'a6.top' was
> generated
> ; By user: shiyong
> (536)
> ; On host: reco.bioinformatics.ku.edu
> <http://reco.bioinformatics.ku.edu>
>
> ; At date: Mon Feb 2 18:00:37
> 2009
> ;
>
> ; This is your topology
> file
> ; "Ease Myself Into the Body Bag" (P.J. Harvey)
> ;
> ; Include forcefield parameters
> #include "ffG53a6.itp"
>
> ; Include chain topologies
> #include "a6_A.itp"
> #include "a6_B.itp"
> #include "a6_C.itp"
>
> ; Include water topology
> #include "spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
> ; Include generic topology for ions
> #include "ions.itp"
>
> [ system ]
> ; Name
> Protein
>
> [ molecules ]
> ; Compound #mols
> Protein_A 1
> Protein_B 1
> Protein_C 1
>
>
> "atoms" section:
>
> Protein_A 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass
> typeB chargeB massB
> 1 NL 1 ASP N 1 0.129 14.0067 ;
> qtot 0.129
> 2 H 1 ASP H1 1 0.248 1.008 ;
> qtot 0.377
> 3 H 1 ASP H2 1 0.248 1.008 ;
> qtot 0.625
> 4 H 1 ASP H3 1 0.248 1.008 ;
> qtot 0.873
> 5 CH1 1 ASP CA 1 0.127 13.019 ;
> qtot 1
> 6 CH2 1 ASP CB 2 0 14.027 ;
> qtot 1
> 7 C 1 ASP CG 3 0.27 12.011 ;
> qtot 1.27
> 8 OM 1 ASP OD1 3 -0.635 15.9994 ;
> qtot 0.635
> 9 OM 1 ASP OD2 3 -0.635 15.9994 ;
> qtot 0
> 10 C 1 ASP C 4 0.45 12.011 ;
> qtot 0.45
> 11 O 1 ASP O 4 -0.45 15.9994 ;
> qtot 0
> 12 N 2 LYSH N 5 -0.31 14.0067 ;
> qtot -0.31
> 13 H 2 LYSH H 5 0.31 1.008 ;
> qtot 0
> 14 CH1 2 LYSH CA 6 0 13.019 ;
> qtot 0
> 15 CH2 2 LYSH CB 6 0 14.027 ;
> qtot 0
> 16 CH2 2 LYSH CG 7 0 14.027 ;
> qtot 0
> 17 CH2 2 LYSH CD 7 0 14.027 ;
> qtot 0
> 18 CH2 2 LYSH CE 8 0.127 14.027 ;
> qtot 0.127
> 19 NL 2 LYSH NZ 8 0.129 14.0067 ;
> qtot 0.256
> 20 H 2 LYSH HZ1 8 0.248 1.008 ;
> qtot 0.504
> 21 H 2 LYSH HZ2 8 0.248 1.008 ;
> qtot 0.752
> 22 H 2 LYSH HZ3 8 0.248 1.008 ;
> qtot 1
> 23 C 2 LYSH C 9 0.45 12.011 ;
> qtot 1.45
> 24 O 2 LYSH O 9 -0.45 15.9994 ;
> qtot 1
>
>
> index groups
>
> [ chAANDB_&_!H* ]
> 1 5 6 7 8 9 10 11 12 14 15 16 17 18 19
> 23 24 25 26 27 28 29 30 31 32 34 35 36 37 38
> 39 40 41 43 44 45 46 48 49 51 52 54 56 58 60
> 61 62 64 65 66 67 68 69 70 71 72 74 75 76 77
> ....
> 2569 2570
>
> [ chC_&_!H* ]
> 2571 2575 2576 2577 2578 2580 2581 2582 2583 2584 2585 2586 2587 2588 2589
> 2590 2591 2592 2593 2594 2595 2597 2598 2599 2600 2601 2602 2605 2606 2607
> ....
>
>
>
>
> On Mon, Feb 2, 2009 at 5:46 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Liu Shiyong wrote:
>
> Here is my command.
>
> pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i
> a6.posre.itp -o
> a6.gro
>
> pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb
>
>
> Why are you running pdb2gmx twice? Unless you have multiple
> proteins, and need multiple topologies, you should not be
> doing this.
>
>
>
> That's because the *.gro file does not include chain id information.
>
> If I run make_ndx -f a6.gro -o a6.ndx
>
> I will get :
>
> Found 0 atoms with chain identifiers A AND B
> >
> Found 0 atoms with chain identifier C
>
>
> 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.
>
>
> editconf -f a6.gro -o a6.gro -d 20.0
>
>
> You realize that the units of -d are nm, right? Do you need
> such a
> huge solute-box distance?
>
> I know the units is nm.
>
>
> Just checking :)
>
>
>
>
> <snip>
>
>
>
> -------------------------------------------------------
> Program grompp, VERSION 4.0.2
> Source code file: grompp.c, line: 150
> Fatal error:
> atoms 1 and 2 in charge group 1 of molecule type
> 'Protein_A' are
> in different energy groups
>
> -------------------------------------------------------
>
>
> 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?
>
> -Justin
>
>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
>
> --
> Shiyong Liu
> Postdoc
> center for bioinformatics in the university of kansas
> Lab: (785)864-1962
> Email: syliu at ku.edu <mailto:syliu at ku.edu> (shiyongliu at ku.edu
> <mailto:shiyongliu at ku.edu> or liushiyong at ku.edu <mailto:liushiyong at ku.edu>)
> Homepage: http://www.people.ku.edu/~syliu
> Lab: http://vakser.bioinformatics.ku.edu/people
> Phone: (785) 864-1962
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
More information about the gromacs.org_gmx-users
mailing list