??????? ???????? 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
--
gmx-users mailing list [email protected]
http://lists.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 [email protected].
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
