h a wrote:
*****************
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.
I would suggest reading the papers that correspond to the Gromos96 force fields,
and united-atom force fields in general.
In addition to the original papers, see here (some references are included):
http://wiki.gromacs.org/index.php/GROMOS
-Justin
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
.
.
.
.
.
************
Thank you so much for your help :)
Sincerely,
Harshith, Under Graduate,
IITK
http://home.iitk.ac.in/~harshith
------------------------------------------------------------------------
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
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