[gmx-users] energy groups
Liu Shiyong
liushiyong at gmail.com
Tue Feb 3 01:08:23 CET 2009
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
; 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> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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--
Shiyong Liu
Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
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