[gmx-users] Adding Na ions to DPPG
Peyman Yamin
Peyman.Yamin at cbi.uni-erlangen.de
Mon Oct 27 14:52:31 CET 2008
Thanks a lot for the replies,
I replace the O in DPPG because I thought it's practical to get the topology
of the quasi-DPPG (which has no charge cause the O is connected to the P)
from prodrg, and then delete the O and replace it with Na and delete the bond
of P with it and try to tell gromacs it's just a non-bonded Na "around" the
P! since it's always around the P replacing the O which was bond to P made
sense to me from the coordinates (distance to P, etc.) point of view. Am I
doing strange things??
I'm not sure if I have to use genion since my zwitterionic DPPG has always its
Na+ beside its O-.
On Monday 27 October 2008 14:03, Justin A. Lemkul wrote:
> Peyman Yamin wrote:
> > Dear GMX users,
> >
> > I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the
> > structure with the Na replaced with O. I get a .top with this from prodrg
> > and try to add the Na manually at the right place by removing the
> > corresponding O. I use GROMOS 96.1 forcefield. GMX version 3.3.1. I have
> > a problem:
>
> Are you trying to replace the O in DPPG with Na+? Or are you simply trying
> to add ions to the surrounding solvent (water)? If you just need ions in
> the solvent, use genion; you don't have to do it manually.
>
> > * In .top file, as far as I can understand, I should just replace OA with
> > NA+ and set the mass and charge.
> > DPPG has a centre: [ O-P(O)=O ] -
> > The Na+ should be around this with +1 charge.
> > should I put charge +1 ?
>
> Again, I'm not clear on what you're trying to accomplish. If you replace
> one of these oxygen atoms, you will likely not have an integer charge
> within the DPPG molecule itself.
I thought since O on P is gone it will be -1 charged, so a +1 Na will balance
it, won't it??
>
> > * which parameters should I place in the top as the Na+ is not bonding. I
> > need LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp.
> > (NA+ OA) but I'm not sure where should I put it in the top file. What
> > should I insert manually in top file at all?
>
> Simply #include "ffG43a1.itp" at the top of your .top file; it will include
> nonbonded and bonded parameters for all the atoms in the system.
Well I do include it. So shouldn't I worry about the nonbonding params and
stuff? like those in topology file? Actually an existential question for me
always is that if everything goes OK by adding the FF itp, then why does
prodrg give me all the params for bonds, dihedrals, angles and etc.??
So, genion or manually replace? and how please...I mean, I don't want to pass
my task to others, but well, a bit of more detailed help would enlight me a
great deal ;)
Cheers,
Peyman
APPENDIX!
***************************** This is the top for the DPPG with the unwanted
O ---> say O number 24. **********************
The question is if I simply change that to Na (of course in pdb as well) what
changes should I make in other switches? I see non of non-bonding context!
(pairs?)
[ moleculetype ]
; Name nrexcl
DRG 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CH3 1 DRG CBL 1 -0.019 15.0350
2 CH2 1 DRG CBK 1 0.006 14.0270
3 CH2 1 DRG CBJ 1 0.006 14.0270
4 CH2 1 DRG CBI 1 0.007 14.0270
5 CH2 1 DRG CBH 2 0.000 14.0270
6 CH2 1 DRG CBG 3 0.000 14.0270
7 CH2 1 DRG CBF 4 0.000 14.0270
8 CH2 1 DRG CBE 5 0.000 14.0270
9 CH2 1 DRG CBD 6 0.000 14.0270
10 CH2 1 DRG CBC 7 0.000 14.0270
11 CH2 1 DRG CBB 8 0.000 14.0270
12 CH2 1 DRG CBA 9 0.000 14.0270
13 CH2 1 DRG CAZ 10 0.039 14.0270
14 CH2 1 DRG CAY 10 0.039 14.0270
15 CH2 1 DRG CAX 10 0.039 14.0270
16 C 1 DRG CAV 10 0.232 12.0110
17 O 1 DRG OAW 10 -0.377 15.9994
18 OA 1 DRG OAU 10 -0.108 15.9994
19 CH1 1 DRG CAT 10 0.136 13.0190
20 CH2 1 DRG CBM 11 0.054 14.0270
21 OA 1 DRG OBN 11 -0.094 15.9994
22 P 1 DRG PBO 11 0.954 30.9738
23 OA 1 DRG OBP 11 -0.410 15.9994
24 OA 1 DRG OBQ 11 -0.410 15.9994
25 OA 1 DRG OBR 11 -0.094 15.9994
26 CH2 1 DRG CBS 12 0.034 14.0270
27 CH1 1 DRG CBT 12 0.070 13.0190
28 OA 1 DRG OBW 12 -0.117 15.9994
29 H 1 DRG HCQ 12 0.013 1.0080
30 CH2 1 DRG CBU 13 0.069 14.0270
31 OA 1 DRG OBV 13 -0.086 15.9994
32 H 1 DRG HCR 13 0.017 1.0080
33 CH2 1 DRG CAS 14 0.145 14.0270
34 OA 1 DRG OAR 14 -0.109 15.9994
35 C 1 DRG CAP 14 0.231 12.0110
36 O 1 DRG OAQ 14 -0.380 15.9994
37 CH2 1 DRG CAO 14 0.038 14.0270
38 CH2 1 DRG CAN 14 0.037 14.0270
39 CH2 1 DRG CAM 14 0.038 14.0270
40 CH2 1 DRG CAL 15 0.000 14.0270
41 CH2 1 DRG CAK 16 0.000 14.0270
42 CH2 1 DRG CAJ 17 0.000 14.0270
43 CH2 1 DRG CAI 18 0.000 14.0270
44 CH2 1 DRG CAH 19 0.000 14.0270
45 CH2 1 DRG CAG 20 0.000 14.0270
46 CH2 1 DRG CAF 21 0.000 14.0270
47 CH2 1 DRG CAE 22 0.000 14.0270
48 CH2 1 DRG CAD 23 0.000 14.0270
49 CH2 1 DRG CAC 24 0.000 14.0270
50 CH2 1 DRG CAB 25 0.000 14.0270
51 CH3 1 DRG CAA 26 0.000 15.0350
[ bonds ]
; ai aj fu c0, c1, ...
2 1 2 0.153 7150000.0 0.153 7150000.0 ; CBK CBL
2 3 2 0.153 7150000.0 0.153 7150000.0 ; CBK CBJ
3 4 2 0.153 7150000.0 0.153 7150000.0 ; CBJ CBI
4 5 2 0.153 7150000.0 0.153 7150000.0 ; CBI CBH
5 6 2 0.153 7150000.0 0.153 7150000.0 ; CBH CBG
6 7 2 0.153 7150000.0 0.153 7150000.0 ; CBG CBF
7 8 2 0.153 7150000.0 0.153 7150000.0 ; CBF CBE
8 9 2 0.153 7150000.0 0.153 7150000.0 ; CBE CBD
9 10 2 0.153 7150000.0 0.153 7150000.0 ; CBD CBC
10 11 2 0.153 7150000.0 0.153 7150000.0 ; CBC CBB
11 12 2 0.153 7150000.0 0.153 7150000.0 ; CBB CBA
12 13 2 0.153 7150000.0 0.153 7150000.0 ; CBA CAZ
13 14 2 0.153 7150000.0 0.153 7150000.0 ; CAZ CAY
14 15 2 0.153 7150000.0 0.153 7150000.0 ; CAY CAX
16 15 2 0.153 7150000.0 0.153 7150000.0 ; CAV CAX
16 17 2 0.123 16600000.0 0.123 16600000.0 ; CAV OAW
16 18 2 0.136 10200000.0 0.136 10200000.0 ; CAV OAU
19 18 2 0.143 8180000.0 0.143 8180000.0 ; CAT OAU
19 20 2 0.153 7150000.0 0.153 7150000.0 ; CAT CBM
19 33 2 0.153 7150000.0 0.153 7150000.0 ; CAT CAS
20 21 2 0.143 8180000.0 0.143 8180000.0 ; CBM OBN
22 21 2 0.161 4840000.0 0.161 4840000.0 ; PBO OBN
22 23 2 0.161 4840000.0 0.161 4840000.0 ; PBO OBP
22 24 2 0.161 4840000.0 0.161 4840000.0 ; PBO OBQ
22 25 2 0.161 4840000.0 0.161 4840000.0 ; PBO OBR
26 25 2 0.143 8180000.0 0.143 8180000.0 ; CBS OBR
27 26 2 0.153 7150000.0 0.153 7150000.0 ; CBT CBS
27 28 2 0.143 8180000.0 0.143 8180000.0 ; CBT OBW
27 30 2 0.153 7150000.0 0.153 7150000.0 ; CBT CBU
28 29 2 0.100 15700000.0 0.100 15700000.0 ; OBW HCQ
30 31 2 0.143 8180000.0 0.143 8180000.0 ; CBU OBV
31 32 2 0.100 15700000.0 0.100 15700000.0 ; OBV HCR
33 34 2 0.143 8180000.0 0.143 8180000.0 ; CAS OAR
35 34 2 0.136 10200000.0 0.136 10200000.0 ; CAP OAR
35 36 2 0.123 16600000.0 0.123 16600000.0 ; CAP OAQ
35 37 2 0.153 7150000.0 0.153 7150000.0 ; CAP CAO
37 38 2 0.153 7150000.0 0.153 7150000.0 ; CAO CAN
38 39 2 0.153 7150000.0 0.153 7150000.0 ; CAN CAM
39 40 2 0.153 7150000.0 0.153 7150000.0 ; CAM CAL
40 41 2 0.153 7150000.0 0.153 7150000.0 ; CAL CAK
41 42 2 0.153 7150000.0 0.153 7150000.0 ; CAK CAJ
42 43 2 0.153 7150000.0 0.153 7150000.0 ; CAJ CAI
43 44 2 0.153 7150000.0 0.153 7150000.0 ; CAI CAH
44 45 2 0.153 7150000.0 0.153 7150000.0 ; CAH CAG
45 46 2 0.153 7150000.0 0.153 7150000.0 ; CAG CAF
46 47 2 0.153 7150000.0 0.153 7150000.0 ; CAF CAE
47 48 2 0.153 7150000.0 0.153 7150000.0 ; CAE CAD
48 49 2 0.153 7150000.0 0.153 7150000.0 ; CAD CAC
49 50 2 0.153 7150000.0 0.153 7150000.0 ; CAC CAB
50 51 2 0.153 7150000.0 0.153 7150000.0 ; CAB CAA
[ pairs ]
; ai aj fu c0, c1, ...
1 4 1 ; CBL CBI
2 5 1 ; CBK CBH
3 6 1 ; CBJ CBG
4 7 1 ; CBI CBF
5 8 1 ; CBH CBE
6 9 1 ; CBG CBD
7 10 1 ; CBF CBC
8 11 1 ; CBE CBB
9 12 1 ; CBD CBA
10 13 1 ; CBC CAZ
11 14 1 ; CBB CAY
12 15 1 ; CBA CAX
13 16 1 ; CAZ CAV
14 17 1 ; CAY OAW
14 18 1 ; CAY OAU
15 19 1 ; CAX CAT
16 20 1 ; CAV CBM
16 33 1 ; CAV CAS
17 19 1 ; OAW CAT
18 21 1 ; OAU OBN
18 34 1 ; OAU OAR
19 22 1 ; CAT PBO
19 35 1 ; CAT CAP
20 23 1 ; CBM OBP
20 24 1 ; CBM OBQ
20 25 1 ; CBM OBR
20 34 1 ; CBM OAR
21 26 1 ; OBN CBS
21 33 1 ; OBN CAS
22 27 1 ; PBO CBT
23 26 1 ; OBP CBS
24 26 1 ; OBQ CBS
25 28 1 ; OBR OBW
25 30 1 ; OBR CBU
26 29 1 ; CBS HCQ
26 31 1 ; CBS OBV
27 32 1 ; CBT HCR
28 31 1 ; OBW OBV
29 30 1 ; HCQ CBU
33 36 1 ; CAS OAQ
33 37 1 ; CAS CAO
34 38 1 ; OAR CAN
35 39 1 ; CAP CAM
36 38 1 ; OAQ CAN
37 40 1 ; CAO CAL
38 41 1 ; CAN CAK
39 42 1 ; CAM CAJ
40 43 1 ; CAL CAI
41 44 1 ; CAK CAH
42 45 1 ; CAJ CAG
43 46 1 ; CAI CAF
44 47 1 ; CAH CAE
45 48 1 ; CAG CAD
46 49 1 ; CAF CAC
47 50 1 ; CAE CAB
48 51 1 ; CAD CAA
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 2 109.5 520.0 109.5 520.0 ; CBL CBK CBJ
2 3 4 2 109.5 520.0 109.5 520.0 ; CBK CBJ CBI
3 4 5 2 109.5 520.0 109.5 520.0 ; CBJ CBI CBH
4 5 6 2 109.5 520.0 109.5 520.0 ; CBI CBH CBG
5 6 7 2 109.5 520.0 109.5 520.0 ; CBH CBG CBF
6 7 8 2 109.5 520.0 109.5 520.0 ; CBG CBF CBE
7 8 9 2 109.5 520.0 109.5 520.0 ; CBF CBE CBD
8 9 10 2 109.5 520.0 109.5 520.0 ; CBE CBD CBC
9 10 11 2 109.5 520.0 109.5 520.0 ; CBD CBC CBB
10 11 12 2 109.5 520.0 109.5 520.0 ; CBC CBB CBA
11 12 13 2 109.5 520.0 109.5 520.0 ; CBB CBA CAZ
12 13 14 2 109.5 520.0 109.5 520.0 ; CBA CAZ CAY
13 14 15 2 109.5 520.0 109.5 520.0 ; CAZ CAY CAX
14 15 16 2 109.5 520.0 109.5 520.0 ; CAY CAX CAV
15 16 17 2 121.0 685.0 121.0 685.0 ; CAX CAV OAW
15 16 18 2 115.0 610.0 115.0 610.0 ; CAX CAV OAU
17 16 18 2 124.0 730.0 124.0 730.0 ; OAW CAV OAU
16 18 19 2 109.5 380.0 109.5 380.0 ; CAV OAU CAT
18 19 20 2 109.5 520.0 109.5 520.0 ; OAU CAT CBM
18 19 33 2 109.5 520.0 109.5 520.0 ; OAU CAT CAS
20 19 33 2 109.5 520.0 109.5 520.0 ; CBM CAT CAS
19 20 21 2 109.5 520.0 109.5 520.0 ; CAT CBM OBN
20 21 22 2 120.0 530.0 120.0 530.0 ; CBM OBN PBO
21 22 23 2 103.0 420.0 103.0 420.0 ; OBN PBO OBP
21 22 24 2 103.0 420.0 103.0 420.0 ; OBN PBO OBQ
21 22 25 2 103.0 420.0 103.0 420.0 ; OBN PBO OBR
23 22 24 2 103.0 420.0 103.0 420.0 ; OBP PBO OBQ
23 22 25 2 103.0 420.0 103.0 420.0 ; OBP PBO OBR
24 22 25 2 103.0 420.0 103.0 420.0 ; OBQ PBO OBR
22 25 26 2 120.0 530.0 120.0 530.0 ; PBO OBR CBS
25 26 27 2 109.5 520.0 109.5 520.0 ; OBR CBS CBT
26 27 28 2 109.5 520.0 109.5 520.0 ; CBS CBT OBW
26 27 30 2 109.5 520.0 109.5 520.0 ; CBS CBT CBU
28 27 30 2 109.5 520.0 109.5 520.0 ; OBW CBT CBU
27 28 29 2 109.5 450.0 109.5 450.0 ; CBT OBW HCQ
27 30 31 2 109.5 520.0 109.5 520.0 ; CBT CBU OBV
30 31 32 2 109.5 450.0 109.5 450.0 ; CBU OBV HCR
19 33 34 2 109.5 520.0 109.5 520.0 ; CAT CAS OAR
33 34 35 2 109.5 380.0 109.5 380.0 ; CAS OAR CAP
34 35 36 2 124.0 730.0 124.0 730.0 ; OAR CAP OAQ
34 35 37 2 115.0 610.0 115.0 610.0 ; OAR CAP CAO
36 35 37 2 121.0 685.0 121.0 685.0 ; OAQ CAP CAO
35 37 38 2 109.5 520.0 109.5 520.0 ; CAP CAO CAN
37 38 39 2 109.5 520.0 109.5 520.0 ; CAO CAN CAM
38 39 40 2 109.5 520.0 109.5 520.0 ; CAN CAM CAL
39 40 41 2 109.5 520.0 109.5 520.0 ; CAM CAL CAK
40 41 42 2 109.5 520.0 109.5 520.0 ; CAL CAK CAJ
41 42 43 2 109.5 520.0 109.5 520.0 ; CAK CAJ CAI
42 43 44 2 109.5 520.0 109.5 520.0 ; CAJ CAI CAH
43 44 45 2 109.5 520.0 109.5 520.0 ; CAI CAH CAG
44 45 46 2 109.5 520.0 109.5 520.0 ; CAH CAG CAF
45 46 47 2 109.5 520.0 109.5 520.0 ; CAG CAF CAE
46 47 48 2 109.5 520.0 109.5 520.0 ; CAF CAE CAD
47 48 49 2 109.5 520.0 109.5 520.0 ; CAE CAD CAC
48 49 50 2 109.5 520.0 109.5 520.0 ; CAD CAC CAB
49 50 51 2 109.5 520.0 109.5 520.0 ; CAC CAB CAA
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
16 15 17 18 2 0.0 167.4 0.0 167.4 ; imp CAV CAX OAW
OAU
19 18 33 20 2 35.3 334.8 35.3 334.8 ; imp CAT OAU CAS
CBM
22 21 24 23 2 35.3 334.8 35.3 334.8 ; imp PBO OBN OBQ
OBP
27 26 28 30 2 35.3 334.8 35.3 334.8 ; imp CBT CBS OBW
CBU
35 34 36 37 2 0.0 167.4 0.0 167.4 ; imp CAP OAR OAQ
CAO
4 3 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih CBI CBJ CBK
CBL
5 4 3 2 1 0.0 5.9 3 0.0 5.9 3 ; dih CBH CBI CBJ
CBK
6 5 4 3 1 0.0 5.9 3 0.0 5.9 3 ; dih CBG CBH CBI
CBJ
7 6 5 4 1 0.0 5.9 3 0.0 5.9 3 ; dih CBF CBG CBH
CBI
8 7 6 5 1 0.0 5.9 3 0.0 5.9 3 ; dih CBE CBF CBG
CBH
9 8 7 6 1 0.0 5.9 3 0.0 5.9 3 ; dih CBD CBE CBF
CBG
10 9 8 7 1 0.0 5.9 3 0.0 5.9 3 ; dih CBC CBD CBE
CBF
11 10 9 8 1 0.0 5.9 3 0.0 5.9 3 ; dih CBB CBC CBD
CBE
12 11 10 9 1 0.0 5.9 3 0.0 5.9 3 ; dih CBA CBB CBC
CBD
13 12 11 10 1 0.0 5.9 3 0.0 5.9 3 ; dih CAZ CBA CBB
CBC
14 13 12 11 1 0.0 5.9 3 0.0 5.9 3 ; dih CAY CAZ CBA
CBB
15 14 13 12 1 0.0 5.9 3 0.0 5.9 3 ; dih CAX CAY CAZ
CBA
16 15 14 13 1 0.0 5.9 3 0.0 5.9 3 ; dih CAV CAX CAY
CAZ
14 15 16 18 1 0.0 1.0 6 0.0 1.0 6 ; dih CAY CAX CAV
OAU
15 16 18 19 1 0.0 3.8 3 0.0 3.8 3 ; dih CAX CAV OAU
CAT
33 19 18 16 1 0.0 3.8 3 0.0 3.8 3 ; dih CAS CAT OAU
CAV
21 20 19 18 1 0.0 5.9 3 0.0 5.9 3 ; dih OBN CBM CAT
OAU
34 33 19 18 1 0.0 5.9 3 0.0 5.9 3 ; dih OAR CAS CAT
OAU
19 20 21 22 1 0.0 1.3 3 0.0 1.3 3 ; dih CAT CBM OBN
PBO
20 21 22 25 1 0.0 3.1 2 0.0 3.1 2 ; dih CBM OBN PBO
OBR
26 25 22 21 1 0.0 3.1 2 0.0 3.1 2 ; dih CBS OBR PBO
OBN
27 26 25 22 1 0.0 1.3 3 0.0 1.3 3 ; dih CBT CBS OBR
PBO
30 27 26 25 1 0.0 5.9 3 0.0 5.9 3 ; dih CBU CBT CBS
OBR
26 27 28 29 1 0.0 1.3 3 0.0 1.3 3 ; dih CBS CBT OBW
HCQ
31 30 27 26 1 0.0 5.9 3 0.0 5.9 3 ; dih OBV CBU CBT
CBS
27 30 31 32 1 0.0 1.3 3 0.0 1.3 3 ; dih CBT CBU OBV
HCR
19 33 34 35 1 0.0 1.3 3 0.0 1.3 3 ; dih CAT CAS OAR
CAP
37 35 34 33 1 0.0 3.8 3 0.0 3.8 3 ; dih CAO CAP OAR
CAS
38 37 35 34 1 0.0 1.0 6 0.0 1.0 6 ; dih CAN CAO CAP
OAR
39 38 37 35 1 0.0 5.9 3 0.0 5.9 3 ; dih CAM CAN CAO
CAP
40 39 38 37 1 0.0 5.9 3 0.0 5.9 3 ; dih CAL CAM CAN
CAO
41 40 39 38 1 0.0 5.9 3 0.0 5.9 3 ; dih CAK CAL CAM
CAN
42 41 40 39 1 0.0 5.9 3 0.0 5.9 3 ; dih CAJ CAK CAL
CAM
43 42 41 40 1 0.0 5.9 3 0.0 5.9 3 ; dih CAI CAJ CAK
CAL
44 43 42 41 1 0.0 5.9 3 0.0 5.9 3 ; dih CAH CAI CAJ
CAK
45 44 43 42 1 0.0 5.9 3 0.0 5.9 3 ; dih CAG CAH CAI
CAJ
46 45 44 43 1 0.0 5.9 3 0.0 5.9 3 ; dih CAF CAG CAH
CAI
47 46 45 44 1 0.0 5.9 3 0.0 5.9 3 ; dih CAE CAF CAG
CAH
48 47 46 45 1 0.0 5.9 3 0.0 5.9 3 ; dih CAD CAE CAF
CAG
49 48 47 46 1 0.0 5.9 3 0.0 5.9 3 ; dih CAC CAD CAE
CAF
50 49 48 47 1 0.0 5.9 3 0.0 5.9 3 ; dih CAB CAC CAD
CAE
51 50 49 48 1 0.0 5.9 3 0.0 5.9 3 ; dih CAA CAB CAC
CAD
************** HERE IS THE PDB *******************
HETATM 1 CBL DRG 1 3.650 5.480 0.060 1.00 20.00
C
HETATM 2 CBK DRG 1 3.740 6.960 0.410 1.00 20.00
C
HETATM 3 CBJ DRG 1 2.330 7.550 0.530 1.00 20.00
C
HETATM 4 CBI DRG 1 2.390 9.040 0.920 1.00 20.00
C
HETATM 5 CBH DRG 1 2.800 9.220 2.380 1.00 20.00
C
HETATM 6 CBG DRG 1 3.160 10.690 2.630 1.00 20.00
C
HETATM 7 CBF DRG 1 3.700 10.840 4.050 1.00 20.00
C
HETATM 8 CBE DRG 1 4.470 12.160 4.170 1.00 20.00
C
HETATM 9 CBD DRG 1 5.960 11.930 4.470 1.00 20.00
C
HETATM 10 CBC DRG 1 6.720 11.320 3.280 1.00 20.00
C
HETATM 11 CBB DRG 1 8.160 10.970 3.640 1.00 20.00
C
HETATM 12 CBA DRG 1 9.060 12.220 3.650 1.00 20.00
C
HETATM 13 CAZ DRG 1 10.520 11.880 4.020 1.00 20.00
C
HETATM 14 CAY DRG 1 11.230 10.990 2.990 1.00 20.00
C
HETATM 15 CAX DRG 1 11.460 11.710 1.660 1.00 20.00
C
HETATM 16 CAV DRG 1 11.440 10.690 0.520 1.00 20.00
C
HETATM 17 OAW DRG 1 12.470 10.380 -0.070 1.00 20.00
O
HETATM 18 OAU DRG 1 10.180 10.230 0.240 1.00 20.00
O
HETATM 19 CAT DRG 1 9.980 9.350 -0.870 1.00 20.00
C
HETATM 20 CBM DRG 1 10.510 7.940 -0.540 1.00 20.00
C
HETATM 21 OBN DRG 1 10.520 7.140 -1.730 1.00 20.00
O
HETATM 22 PBO DRG 1 10.640 5.530 -1.680 1.00 20.00
P
HETATM 23 OBP DRG 1 10.740 4.990 -3.190 1.00 20.00
O
HETATM 24 OBQ DRG 1 11.950 5.090 -0.860 1.00 20.00
O
HETATM 25 OBR DRG 1 9.310 4.920 -1.020 1.00 20.00
O
HETATM 26 CBS DRG 1 9.240 3.550 -0.600 1.00 20.00
C
HETATM 27 CBT DRG 1 8.120 3.340 0.440 1.00 20.00
C
HETATM 28 OBW DRG 1 6.870 3.840 -0.040 1.00 20.00
O
HETATM 29 HCQ DRG 1 6.170 3.720 0.660 1.00 20.00
H
HETATM 30 CBU DRG 1 8.460 3.970 1.800 1.00 20.00
C
HETATM 31 OBV DRG 1 8.620 5.390 1.750 1.00 20.00
O
HETATM 32 HCR DRG 1 7.800 5.810 1.370 1.00 20.00
H
HETATM 33 CAS DRG 1 8.450 9.340 -1.060 1.00 20.00
C
HETATM 34 OAR DRG 1 7.970 8.440 -2.070 1.00 20.00
O
HETATM 35 CAP DRG 1 7.270 7.370 -1.600 1.00 20.00
C
HETATM 36 OAQ DRG 1 7.340 6.950 -0.440 1.00 20.00
O
HETATM 37 CAO DRG 1 6.380 6.600 -2.580 1.00 20.00
C
HETATM 38 CAN DRG 1 6.800 6.550 -4.060 1.00 20.00
C
HETATM 39 CAM DRG 1 6.680 7.890 -4.820 1.00 20.00
C
HETATM 40 CAL DRG 1 5.330 8.630 -4.730 1.00 20.00
C
HETATM 41 CAK DRG 1 4.160 8.020 -5.510 1.00 20.00
C
HETATM 42 CAJ DRG 1 3.360 7.030 -4.660 1.00 20.00
C
HETATM 43 CAI DRG 1 2.050 6.620 -5.330 1.00 20.00
C
HETATM 44 CAH DRG 1 1.000 7.740 -5.190 1.00 20.00
C
HETATM 45 CAG DRG 1 -0.350 7.340 -5.790 1.00 20.00
C
HETATM 46 CAF DRG 1 -1.070 6.230 -5.010 1.00 20.00
C
HETATM 47 CAE DRG 1 -1.570 6.730 -3.640 1.00 20.00
C
HETATM 48 CAD DRG 1 -2.220 5.590 -2.830 1.00 20.00
C
HETATM 49 CAC DRG 1 -1.280 4.970 -1.790 1.00 20.00
C
HETATM 50 CAB DRG 1 -0.260 3.990 -2.400 1.00 20.00
C
HETATM 51 CAA DRG 1 0.600 3.390 -1.290 1.00 20.00
C
CONECT 1 2
CONECT 2 1 3
CONECT 3 2 4
CONECT 4 3 5
CONECT 5 4 6
CONECT 6 5 7
CONECT 7 6 8
CONECT 8 7 9
CONECT 9 8 10
CONECT 10 9 11
CONECT 11 10 12
CONECT 12 11 13
CONECT 13 12 14
CONECT 14 13 15
CONECT 15 14 16
CONECT 16 15 17 18
CONECT 17 16
CONECT 18 16 19
CONECT 19 18 20 33
CONECT 20 19 21
CONECT 21 20 22
CONECT 22 21 23 24 25
CONECT 23 22
CONECT 24 22
CONECT 25 22 26
CONECT 26 25 27
CONECT 27 26 28 30
CONECT 28 27 29
CONECT 29 28
CONECT 30 27 31
CONECT 31 30 32
CONECT 32 31
CONECT 33 19 34
CONECT 34 33 35
CONECT 35 34 36 37
CONECT 36 35
CONECT 37 35 38
CONECT 38 37 39
CONECT 39 38 40
CONECT 40 39 41
CONECT 41 40 42
CONECT 42 41 43
CONECT 43 42 44
CONECT 44 43 45
CONECT 45 44 46
CONECT 46 45 47
CONECT 47 46 48
CONECT 48 47 49
CONECT 49 48 50
CONECT 50 49 51
CONECT 51 50
END
>
> -Justin
>
> > Thanks in advance for the time,
> > I've been away for some time from GMX and might sound
> >
> > Cheers,
> > Peyman
--
Peyman Yamin
Lehrstuhl fuer Thermische Verfahrenstechnik
Universitaet Erlangen-Nuernberg
Egerlandstr. 3
91058 Erlangen
Phone: +49(0) - 9131 - 85 27671
Mailto: peyman.yamin at cbi.uni-erlangen.de
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