[gmx-users] 2 questions

Алексей Раевский rayevsky85 at gmail.com
Tue Dec 8 01:15:29 CET 2009

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?

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! 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:

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 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








CG1 HG11

CG1 HG12

CG1 HG13

CG2 HG21

CG2 HG22

CG2 HG23


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


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...
Please, help me.
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