Dear Users,
I used prodrg( gomos96.1) to generate topology and .gro files of polystyrene
( of 10 monomers ). the read me file is as shown
*****
DRGFIN.PDB : the final PDB file with all hydrogens added
DRGPOH.PDB : the final PDB file with only polar hydrogens added
DRGNOH.PDB : the final PDB file without any hydrogens added
DRGFIN.MOL : the final Molfile with all hydrogens added
DRGPOH.MOL : the final Molfile with only polar hydrogens added
DRGNOH.MOL : the final Molfile without any hydrogens added
DRGFIN.GRO : final coordinates in GROMOS87 format (all hydrogens)
DRGPOH.GRO : final coordinates in GROMOS87 format (polar hydrogens only)
DRGCNS.PAR : CNS parameter file
DRGCNS.TOP : CNS topology file
DRGMAC.LIB : REFMAC5 library
DRGSHX.TOP : SHELX topology
DRGTRS.O : O <9.0 torsion database (read in with: read DRGTRS.O in O)
DRGFNOH.O6 : O <9.0 refi dictionary
DRGNOH.O : O 9.x dictionary
DRGGMX.ITP : GROMACS .itp file
DRGWIF.TOP : WHAT IF topology
DRGFIN.MOL2 : SYBYL2 file with all hydrogens
DRGPOH.MOL2 : SYBYL2 file with only polar hydrogens
DRGAD2.PDBQ : AutoDock 2.4 PDBQ file
DRGAD3.PDBQ : AutoDock 3.0 PDBQ file
DRGHEX.TOP : HEX topology
*****************
Now I'm actually studying protein polymer_surface interactions, using g43a1
forcefield . Can anybody explain whether should I use polymer model with
only polar hydrogens or polymer model with all hydrogens ? What is the
significance of these hydrogens.
In the .itp file(shown below) there are 130 atoms but total number of atoms
in only polar hydrogens model is 80 same with no hydrogens model. Including
all hydrogens I have 162 atoms. So what does this 130 correspond to ?? (
actually I'm facing fatal error because of this consistency in number of
atoms while doing EM )
*******
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CR1 1 STY CAB 1 -0.006 12.0110
2 HC 1 STY HAB 1 0.006 1.0080
3 CR1 1 STY CAC 2 -0.016 12.0110
4 HC 1 STY HAC 2 0.002 1.0080
5 CR1 1 STY CAD 2 -0.017 12.0110
6 HC 1 STY HAD 2 0.002 1.0080
7 CR1 1 STY CAE 2 -0.017 12.0110
8 HC 1 STY HAE 2 0.002 1.0080
9 CR1 1 STY CAF 2 -0.017 12.0110
10 HC 1 STY HAF 2 0.002 1.0080
11 C 1 STY CAA 2 -0.025 12.0110
12 CH1 1 STY CAG 2 0.067 13.0190
13 CH3 1 STY CAH 2 0.017 15.0350
14 CH2 1 STY CAP 3 0.000 14.0270
15 CH1 1 STY CAO 4 0.060 13.0190
16 C 1 STY CAI 4 -0.027 12.0110
17 CR1 1 STY CAJ 4 -0.018 12.0110
18 HC 1 STY HAK 4 0.001 1.0080
19 CR1 1 STY CAK 4 -0.018 12.0110
20 HC 1 STY HAL 4 0.002 1.0080
21 CR1 1 STY CAL 5 -0.016 12.0110
22 HC 1 STY HAM 5 0.003 1.0080
23 CR1 1 STY CAM 5 -0.016 12.0110
24 HC 1 STY HAN 5 0.003 1.0080
25 CR1 1 STY CAN 5 -0.016 12.0110
26 HC 1 STY HAO 5 0.003 1.0080
27 CH2 1 STY CAX 5 0.039 14.0270
28 CH1 1 STY CAW 6 0.060 13.0190
29 C 1 STY CAQ 6 -0.027 12.0110
30 CR1 1 STY CAR 6 -0.018 12.0110
31 HC 1 STY HAS 6 0.001 1.0080
32 CR1 1 STY CAS 6 -0.018 12.0110
33 HC 1 STY HAT 6 0.002 1.0080
34 CR1 1 STY CAT 7 -0.016 12.0110
35 HC 1 STY HAU 7 0.003 1.0080
36 CR1 1 STY CAU 7 -0.016 12.0110
37 HC 1 STY HAV 7 0.003 1.0080
38 CR1 1 STY CAV 7 -0.016 12.0110
39 HC 1 STY HAW 7 0.003 1.0080
40 CH2 1 STY CBF 7 0.039 14.0270
41 CH1 1 STY CBE 8 0.060 13.0190
42 C 1 STY CAY 8 -0.027 12.0110
43 CR1 1 STY CAZ 8 -0.018 12.0110
44 HC 1 STY HA0 8 0.001 1.0080
45 CR1 1 STY CBA 8 -0.018 12.0110
46 HC 1 STY HBA 8 0.002 1.0080
47 CR1 1 STY CBB 9 -0.016 12.0110
48 HC 1 STY HBB 9 0.003 1.0080
49 CR1 1 STY CBC 9 -0.016 12.0110
50 HC 1 STY HBC 9 0.003 1.0080
51 CR1 1 STY CBD 9 -0.016 12.0110
52 HC 1 STY HBD 9 0.003 1.0080
53 CH2 1 STY CBN 9 0.039 14.0270
54 CH1 1 STY CBM 10 0.060 13.0190
55 C 1 STY CBG 10 -0.027 12.0110
56 CR1 1 STY CBH 10 -0.018 12.0110
57 HC 1 STY HBH 10 0.001 1.0080
58 CR1 1 STY CBI 10 -0.018 12.0110
59 HC 1 STY HBI 10 0.002 1.0080
60 CR1 1 STY CBJ 11 -0.016 12.0110
61 HC 1 STY HBJ 11 0.003 1.0080
62 CR1 1 STY CBK 11 -0.016 12.0110
63 HC 1 STY HBK 11 0.003 1.0080
64 CR1 1 STY CBL 11 -0.016 12.0110
65 HC 1 STY HBL 11 0.003 1.0080
66 CH2 1 STY CBV 11 0.039 14.0270
67 CH1 1 STY CBU 12 0.060 13.0190
68 C 1 STY CBO 12 -0.027 12.0110
69 CR1 1 STY CBP 12 -0.018 12.0110
70 HC 1 STY HBP 12 0.001 1.0080
71 CR1 1 STY CBQ 12 -0.018 12.0110
72 HC 1 STY HBQ 12 0.002 1.0080
73 CR1 1 STY CBR 13 -0.016 12.0110
74 HC 1 STY HBR 13 0.003 1.0080
75 CR1 1 STY CBS 13 -0.016 12.0110
76 HC 1 STY HBS 13 0.003 1.0080
77 CR1 1 STY CBT 13 -0.016 12.0110
78 HC 1 STY HBT 13 0.003 1.0080
79 CH2 1 STY CCD 13 0.039 14.0270
80 CH1 1 STY CCC 14 0.060 13.0190
81 C 1 STY CBW 14 -0.027 12.0110
82 CR1 1 STY CBX 14 -0.018 12.0110
83 HC 1 STY HBX 14 0.001 1.0080
84 CR1 1 STY CBY 14 -0.018 12.0110
85 HC 1 STY HBY 14 0.002 1.0080
86 CR1 1 STY CBZ 15 -0.016 12.0110
87 HC 1 STY HBZ 15 0.003 1.0080
88 CR1 1 STY CCA 15 -0.016 12.0110
89 HC 1 STY HCA 15 0.003 1.0080
90 CR1 1 STY CCB 15 -0.016 12.0110
91 HC 1 STY HCB 15 0.003 1.0080
92 CH2 1 STY CCL 15 0.039 14.0270
93 CH1 1 STY CCK 16 0.060 13.0190
94 C 1 STY CCE 16 -0.027 12.0110
95 CR1 1 STY CCF 16 -0.018 12.0110
96 HC 1 STY HCF 16 0.001 1.0080
97 CR1 1 STY CCG 16 -0.018 12.0110
98 HC 1 STY HCG 16 0.002 1.0080
99 CR1 1 STY CCH 17 -0.016 12.0110
100 HC 1 STY HCH 17 0.003 1.0080
101 CR1 1 STY CCI 17 -0.016 12.0110
102 HC 1 STY HCI 17 0.003 1.0080
103 CR1 1 STY CCJ 17 -0.016 12.0110
104 HC 1 STY HCJ 17 0.003 1.0080
105 CH2 1 STY CCT 17 0.039 14.0270
106 CH1 1 STY CCS 18 0.060 13.0190
107 C 1 STY CCM 18 -0.027 12.0110
108 CR1 1 STY CCN 18 -0.018 12.0110
109 HC 1 STY HCN 18 0.001 1.0080
110 CR1 1 STY CCO 18 -0.018 12.0110
111 HC 1 STY HCO 18 0.002 1.0080
112 CR1 1 STY CCP 19 -0.016 12.0110
113 HC 1 STY HCP 19 0.003 1.0080
114 CR1 1 STY CCQ 19 -0.016 12.0110
115 HC 1 STY HCQ 19 0.003 1.0080
116 CR1 1 STY CCR 19 -0.016 12.0110
117 HC 1 STY HCR 19 0.003 1.0080
118 CH2 1 STY CDB 19 0.039 14.0270
119 CH2 1 STY CDA 20 0.066 14.0270
120 C 1 STY CCU 20 -0.019 12.0110
121 CR1 1 STY CCV 20 -0.012 12.0110
122 HC 1 STY HCV 20 0.003 1.0080
123 CR1 1 STY CCW 20 -0.013 12.0110
124 HC 1 STY HCW 20 0.004 1.0080
125 CR1 1 STY CCX 20 -0.013 12.0110
126 HC 1 STY HCX 20 0.004 1.0080
127 CR1 1 STY CCY 20 -0.013 12.0110
128 HC 1 STY HCY 20 0.003 1.0080
129 CR1 1 STY CCZ 20 -0.013 12.0110
130 HC 1 STY HCZ 20 0.003 1.0080
[ bonds ]
; ai aj fu c0, c1, ...
1 2 2 0.109 12300000.0 0.109 12300000.0 ; CAB HAB
1 3 2 0.139 10800000.0 0.139 10800000.0 ; CAB CAC
.
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************
Thank you so much for your help :)
Sincerely,
Harshith, Under Graduate,
IITK
http://home.iitk.ac.in/~harshith
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