[gmx-users] 2 questions

Tue Dec 8 04:46:45 CET 2009

??????? ???????? wrote:
> Hi all.
> 
> I'm working with gromacs 4.0.5 in amber99 force field. I have two questions:
> 
> 1. The protein part of my complex (trna+protein) consists of 870 
> aminoacids and two atoms of Zn. The question is - whether I have to 
> create an index file, which will unit aminoacids and Zn in one "protein" 
> or not? If not - whether those Zn will be stable during dynamics or they 
> will escape from the structure in the water?

Index files create artificial groupings for MD algorithms or analysis 
tools, they don't have any direct effect on the physics. The Zn will be 
stable if you have constructed a reasonable physical model of a stable 
Zn complex. Often this is hard to do with an MM force field. Consult the 
literature - Zn+na has surely been done lots of times.

> 2. One of the goals of my work is studing of aminoacyl-adenylat behavior:
> 
> look, when I added aminoacid to adenyn through O2' in hyperchem and then 
> created topology everything was fine untill I get to dynamics (even 
> steep and gradient)... results I saw were very bad, aminoacid flied away 
> from adenyn...I thought gromacs doesn't see this bond between aminoacid 
> and nucleotide...saw I created a new topology for it!

If it flies away, then the physics is such that it doesn't want to be 
nearby. Whatever you did in hyperchem will have nothing to do with 
whether you generated a topology with a covalently bound complex. That 
depends on your use of pdb2gmx and/or subsequent manipulation of the 
.top file.

> It represents both 
> elements (aa and nucleotide) as a one. And I have written a new bond in 
> ff...bon.itp . This is examples of my work - fragments of a) .rtp, b) 
> .hdb, c) ff..bon.itp:

I can't make any sense of this because you've not described your 
objective well enough. Is there a covalent bond between two moieties, or 
what? If so, where? Upload a screenshot from hyperchem if suitable.

> a)[ RA3 ]
> 
> [ atoms ]
> 
> N amber99_39 0.05770 1
> 
> H9 amber99_24 0.22720 2
> 
> CA amber99_11 -0.00540 3
> 
> HA amber99_28 0.10930 4
> 
> CB amber99_11 0.31960 5
> 
> HB amber99_18 -0.02210 6
> 
> CG1 amber99_11 -0.31290 7
> 
> HG11 amber99_18 0.07350 8
> 
> HG12 amber99_18 0.07350 9
> 
> HG13 amber99_18 0.07350 10
> 
> CG2 amber99_11 -0.31290 11
> 
> HG21 amber99_18 0.07350 12
> 
> HG22 amber99_18 0.07350 13
> 
> HG23 amber99_18 0.07350 14
> 
> C amber99_2 0.61630 15
> 
> O amber99_41 -0.57220 16
> 
> P amber99_46 1.16620 17
> 
> O1P amber99_45 -0.77600 18
> 
> O2P amber99_45 -0.77600 19
> 
> O5' amber99_44 -0.49890 20
> 
> C5' amber99_11 0.05580 21
> 
> H5'1 amber99_19 0.06790 22
> 
> H5'2 amber99_19 0.06790 23
> 
> C4' amber99_11 0.10650 24
> 
> H4' amber99_19 0.11740 25
> 
> O4' amber99_44 -0.35480 26
> 
> C1' amber99_11 0.03940 27
> 
> H1' amber99_20 0.20070 28
> 
> N9 amber99_40 -0.02510 29
> 
> C8 amber99_6 0.20060 30
> 
> H8 amber99_24 0.15530 31
> 
> N7 amber99_36 -0.60730 32
> 
> C5 amber99_4 0.05150 33
> 
> C6 amber99_3 0.70090 34
> 
> N6 amber99_38 -0.90190 35
> 
> H61 amber99_17 0.41150 36
> 
> H62 amber99_17 0.41150 37
> 
> N1 amber99_37 -0.76150 38
> 
> C2 amber99_9 0.58750 39
> 
> N3 amber99_37 -0.69970 40
> 
> C4 amber99_4 0.30530 41
> 
> C3' amber99_11 0.20220 42
> 
> H3' amber99_19 0.06150 43
> 
> C2' amber99_11 0.06700 44
> 
> H2'1 amber99_19 0.09720 45
> 
> O2' amber99_44 -0.61390 46
> 
> HO'2 amber99_25 0.41860 47
> 
> O3' amber99_43 -0.65410 48
> 
> H1 amber99_17 0.22720 49
> 
> H2 amber99_17 0.22720 50
> 
> H3 amber99_17 0.22720 51
> 
> [ bonds ]
> 
> P O1P
> 
> P O2P
> 
> P O5'
> 
> O5' C5'
> 
> C5' H5'1
> 
> C5' H5'2
> 
> C5' C4'
> 
> C4' H4'
> 
> C4' O4'
> 
> C4' C3'
> 
> O4' C1'
> 
> C1' H1'
> 
> C1' N9
> 
> C1' C2'
> 
> N9 C8
> 
> N9 C4
> 
> C8 H8
> 
> C8 N7
> 
> N7 C5
> 
> C5 C6
> 
> C5 C4
> 
> C6 N6
> 
> C6 N1
> 
> N6 H61
> 
> N6 H62
> 
> N1 C2
> 
> C2 H9
> 
> C2 N3
> 
> N3 C4
> 
> C3' H3'
> 
> C3' C2'
> 
> C3' O3'
> 
> C2' H2'1
> 
> C2' O2'
> 
> O3' HO'2
> 
> O2' C
> 
> -O3' P
> 
> N H1
> 
> N H2
> 
> N H3
> 
> N CA
> 
> CA HA
> 
> CA CB
> 
> CA C
> 
> CB HB
> 
> CB CG1
> 
> CB CG2
> 
> CG1 HG11
> 
> CG1 HG12
> 
> CG1 HG13
> 
> CG2 HG21
> 
> CG2 HG22
> 
> CG2 HG23
> 
> C O
> 
> C +N
> 
> [ dihedrals ]
> 
> O4' C1' N9 C4 proper_X_CT_N*_X
> 
> C1' N9 C8 H8 proper_X_CK_N*_X
> 
> C1' N9 C8 N7 proper_X_CK_N*_X
> 
> C1' N9 C4 C5 proper_X_CB_N*_X
> 
> C1' N9 C4 N3 proper_X_CB_N*_X
> 
> H1' C1' N9 C8 proper_X_CT_N*_X
> 
> H1' C1' N9 C4 proper_X_CT_N*_X
> 
> C8 N9 C4 C5 proper_X_CB_N*_X
> 
> C8 N9 C4 N3 proper_X_CB_N*_X
> 
> C5 C6 N1 C2 proper_X_CA_NC_X
> 
> N6 C6 N1 C2 proper_X_CA_NC_X
> 
> N1 C2 N3 C4 proper_X_CQ_NC_X
> 
> H9 C2 N3 C4 proper_X_CQ_NC_X
> 
> H8 C8 N7 C5 proper_X_CK_NB_X
> 
> N9 C8 N7 C5 proper_X_CK_NB_X
> 
> H62 N6 C6 N1 proper_X_CA_N2_X
> 
> H61 N6 C6 N1 proper_X_CA_N2_X
> 
> C5 C6 N6 H61 proper_X_CA_N2_X
> 
> C5 C6 N6 H62 proper_X_CA_N2_X
> 
> H8 C8 N9 C4 proper_X_CK_N*_X
> 
> N7 C8 N9 C4 proper_X_CK_N*_X
> 
> O5' C5' C4' H4' proper_H_CT_CT_O
> 
> H5'1 C5' C4' O4' proper_H_CT_CT_O
> 
> H5'2 C5' C4' O4' proper_H_CT_CT_O
> 
> O4' C4' C3' H3' proper_H_CT_CT_O
> 
> O4' C1' C2' H2'1 proper_H_CT_CT_O
> 
> C2' O2' C CA proper_H_CT_CT_O
> 
> CA C +N +H backbone_prop_1
> 
> O C +N +H backbone_prop_2
> 
> CA C +N +CA backbone_prop_1
> 
> O C +N +CA backbone_prop_1
> 
> [ impropers ]
> 
> C4 C8 N9 C1' nucleic_imp_10
> 
> C6 H61 N6 H62
> 
> N9 N7 C8 H8
> 
> N1 N3 C2 H9 nucleic_imp_11
> 
> C5 N6 C6 N1 nucleic_imp_11
> 
> CA +N C O
> 
> b)RA3 14
> 
> 2 6 H5' C5' O5' C4'
> 
> 1 5 H4' C4' C5' O4' C3'
> 
> 1 5 H1' C1' O4' N9 C2'
> 
> 1 1 H8 C8 N9 N7
> 
> 2 3 H6 N6 C6 C5
> 
> 1 1 H9 C2 N1 N3
> 
> 1 5 H3' C3' C4' C2' O3'
> 
> 1 5 H2'1 C2' C1' C3' O2'
> 
> 1 2 HO'2 O3' C3' C4'
> 
> 3 4 H N CA CB
> 
> 1 5 HA CA N CB C
> 
> 1 5 HB CB CA CG1 CG2
> 
> 3 4 HG1 CG1 CB CA
> 
> 3 4 HG2 CG2 CB CA
> 
> c)CT OS C 1 109.500 502.080 ;
> 
> (
> 
> amber99_11 12.01000 ; CT sp3 aliphatic C/
> 
> amber99_44 16.00000 ; OS ether and ester oxygen/
> 
> amber99_2 12.01000 ; C sp2 C carbonyl group/)
> 
> The problem is that, when I tried molecule of aminoacyladenylate in 
> dynamics - everything is ok. But in complex there a lot of warnings and 
> errors with pdb2gmx topology creating. First of all, when I did my first 
> efforts I described above ("when I added aminoacid to adenyn through O2' 
> in hyperchem and then created topology everything was fine untill I get 
> to dynamics") I had atom name O2 in RC and RU (cytozine, uracyl) in pdb 
> file and had no problems, but now gromacs couldn't find it, and I saw 
> that in .rtp it has name "O"...ok, I changed all O2 in cytozynes and 
> uracyls...gromacs is satisfied with but it is an error in aa
> 
> No !random acid! it depends on time I run pdb2gmx, every time another 
> atom not found while adding hydrogens. I'm sure that atom names 
> corresponds to each other in pdb and in hdb or rtp base...If I make a 
> little changes in coordinates of this atom - other atom in some acid is 
> bad...and so on, untill I have got an error
> 
> Source code file: pgutil.c, line: 87
> 
> Fatal error: atom N not found in residue -1072258112 while adding 
> impropers (I eve can't find this atom). -missing - is ok. But on the 
> stage of grompp I got an error "no default angle", without any 
> explanations...

It's all too confused, sorry :-)

Mark