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: [EMAIL PROTECTED] _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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