Dear Users,<br><br>I used prodrg( gomos96.1) to generate topology and .gro files of polystyrene ( of 10 monomers ). the read me file is as shown <br>*****<br>DRGFIN.PDB : the final PDB file with all hydrogens added<br>DRGPOH.PDB : the final PDB file with only polar hydrogens added<br>
DRGNOH.PDB : the final PDB file without any hydrogens added<br><br>DRGFIN.MOL : the final Molfile with all hydrogens added<br>DRGPOH.MOL : the final Molfile with only polar hydrogens added<br>DRGNOH.MOL : the final Molfile without any hydrogens added<br>
<br>DRGFIN.GRO : final coordinates in GROMOS87 format (all hydrogens)<br>DRGPOH.GRO : final coordinates in GROMOS87 format (polar hydrogens only)<br><br>DRGCNS.PAR : CNS parameter file<br>DRGCNS.TOP : CNS topology file<br>
<br>DRGMAC.LIB : REFMAC5 library<br><br>DRGSHX.TOP : SHELX topology<br><br>DRGTRS.O : O <9.0 torsion database (read in with: read DRGTRS.O in O)<br>DRGFNOH.O6 : O <9.0 refi dictionary<br>DRGNOH.O : O 9.x dictionary<br>
<br>DRGGMX.ITP : GROMACS .itp file<br><br>DRGWIF.TOP : WHAT IF topology<br><br>DRGFIN.MOL2 : SYBYL2 file with all hydrogens<br>DRGPOH.MOL2 : SYBYL2 file with only polar hydrogens<br><br>DRGAD2.PDBQ : AutoDock 2.4 PDBQ file<br>
DRGAD3.PDBQ : AutoDock 3.0 PDBQ file<br><br>DRGHEX.TOP : HEX topology<br>*****************<br><br>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. <br>
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 )<br>
*******<br>[ atoms ]<br>; nr type resnr resid atom cgnr charge mass<br> 1 CR1 1 STY CAB 1 -0.006 12.0110 <br> 2 HC 1 STY HAB 1 0.006 1.0080 <br> 3 CR1 1 STY CAC 2 -0.016 12.0110 <br>
4 HC 1 STY HAC 2 0.002 1.0080 <br> 5 CR1 1 STY CAD 2 -0.017 12.0110 <br> 6 HC 1 STY HAD 2 0.002 1.0080 <br> 7 CR1 1 STY CAE 2 -0.017 12.0110 <br>
8 HC 1 STY HAE 2 0.002 1.0080 <br> 9 CR1 1 STY CAF 2 -0.017 12.0110 <br> 10 HC 1 STY HAF 2 0.002 1.0080 <br> 11 C 1 STY CAA 2 -0.025 12.0110 <br>
12 CH1 1 STY CAG 2 0.067 13.0190 <br> 13 CH3 1 STY CAH 2 0.017 15.0350 <br> 14 CH2 1 STY CAP 3 0.000 14.0270 <br> 15 CH1 1 STY CAO 4 0.060 13.0190 <br>
16 C 1 STY CAI 4 -0.027 12.0110 <br> 17 CR1 1 STY CAJ 4 -0.018 12.0110 <br> 18 HC 1 STY HAK 4 0.001 1.0080 <br> 19 CR1 1 STY CAK 4 -0.018 12.0110 <br>
20 HC 1 STY HAL 4 0.002 1.0080 <br> 21 CR1 1 STY CAL 5 -0.016 12.0110 <br> 22 HC 1 STY HAM 5 0.003 1.0080 <br> 23 CR1 1 STY CAM 5 -0.016 12.0110 <br>
24 HC 1 STY HAN 5 0.003 1.0080 <br> 25 CR1 1 STY CAN 5 -0.016 12.0110 <br> 26 HC 1 STY HAO 5 0.003 1.0080 <br> 27 CH2 1 STY CAX 5 0.039 14.0270 <br>
28 CH1 1 STY CAW 6 0.060 13.0190 <br> 29 C 1 STY CAQ 6 -0.027 12.0110 <br> 30 CR1 1 STY CAR 6 -0.018 12.0110 <br> 31 HC 1 STY HAS 6 0.001 1.0080 <br>
32 CR1 1 STY CAS 6 -0.018 12.0110 <br> 33 HC 1 STY HAT 6 0.002 1.0080 <br> 34 CR1 1 STY CAT 7 -0.016 12.0110 <br> 35 HC 1 STY HAU 7 0.003 1.0080 <br>
36 CR1 1 STY CAU 7 -0.016 12.0110 <br> 37 HC 1 STY HAV 7 0.003 1.0080 <br> 38 CR1 1 STY CAV 7 -0.016 12.0110 <br> 39 HC 1 STY HAW 7 0.003 1.0080 <br>
40 CH2 1 STY CBF 7 0.039 14.0270 <br> 41 CH1 1 STY CBE 8 0.060 13.0190 <br> 42 C 1 STY CAY 8 -0.027 12.0110 <br> 43 CR1 1 STY CAZ 8 -0.018 12.0110 <br>
44 HC 1 STY HA0 8 0.001 1.0080 <br> 45 CR1 1 STY CBA 8 -0.018 12.0110 <br> 46 HC 1 STY HBA 8 0.002 1.0080 <br> 47 CR1 1 STY CBB 9 -0.016 12.0110 <br>
48 HC 1 STY HBB 9 0.003 1.0080 <br> 49 CR1 1 STY CBC 9 -0.016 12.0110 <br> 50 HC 1 STY HBC 9 0.003 1.0080 <br> 51 CR1 1 STY CBD 9 -0.016 12.0110 <br>
52 HC 1 STY HBD 9 0.003 1.0080 <br> 53 CH2 1 STY CBN 9 0.039 14.0270 <br> 54 CH1 1 STY CBM 10 0.060 13.0190 <br> 55 C 1 STY CBG 10 -0.027 12.0110 <br>
56 CR1 1 STY CBH 10 -0.018 12.0110 <br> 57 HC 1 STY HBH 10 0.001 1.0080 <br> 58 CR1 1 STY CBI 10 -0.018 12.0110 <br> 59 HC 1 STY HBI 10 0.002 1.0080 <br>
60 CR1 1 STY CBJ 11 -0.016 12.0110 <br> 61 HC 1 STY HBJ 11 0.003 1.0080 <br> 62 CR1 1 STY CBK 11 -0.016 12.0110 <br> 63 HC 1 STY HBK 11 0.003 1.0080 <br>
64 CR1 1 STY CBL 11 -0.016 12.0110 <br> 65 HC 1 STY HBL 11 0.003 1.0080 <br> 66 CH2 1 STY CBV 11 0.039 14.0270 <br> 67 CH1 1 STY CBU 12 0.060 13.0190 <br>
68 C 1 STY CBO 12 -0.027 12.0110 <br> 69 CR1 1 STY CBP 12 -0.018 12.0110 <br> 70 HC 1 STY HBP 12 0.001 1.0080 <br> 71 CR1 1 STY CBQ 12 -0.018 12.0110 <br>
72 HC 1 STY HBQ 12 0.002 1.0080 <br> 73 CR1 1 STY CBR 13 -0.016 12.0110 <br> 74 HC 1 STY HBR 13 0.003 1.0080 <br> 75 CR1 1 STY CBS 13 -0.016 12.0110 <br>
76 HC 1 STY HBS 13 0.003 1.0080 <br> 77 CR1 1 STY CBT 13 -0.016 12.0110 <br> 78 HC 1 STY HBT 13 0.003 1.0080 <br> 79 CH2 1 STY CCD 13 0.039 14.0270 <br>
80 CH1 1 STY CCC 14 0.060 13.0190 <br> 81 C 1 STY CBW 14 -0.027 12.0110 <br> 82 CR1 1 STY CBX 14 -0.018 12.0110 <br> 83 HC 1 STY HBX 14 0.001 1.0080 <br>
84 CR1 1 STY CBY 14 -0.018 12.0110 <br> 85 HC 1 STY HBY 14 0.002 1.0080 <br> 86 CR1 1 STY CBZ 15 -0.016 12.0110 <br> 87 HC 1 STY HBZ 15 0.003 1.0080 <br>
88 CR1 1 STY CCA 15 -0.016 12.0110 <br> 89 HC 1 STY HCA 15 0.003 1.0080 <br> 90 CR1 1 STY CCB 15 -0.016 12.0110 <br> 91 HC 1 STY HCB 15 0.003 1.0080 <br>
92 CH2 1 STY CCL 15 0.039 14.0270 <br> 93 CH1 1 STY CCK 16 0.060 13.0190 <br> 94 C 1 STY CCE 16 -0.027 12.0110 <br> 95 CR1 1 STY CCF 16 -0.018 12.0110 <br>
96 HC 1 STY HCF 16 0.001 1.0080 <br> 97 CR1 1 STY CCG 16 -0.018 12.0110 <br> 98 HC 1 STY HCG 16 0.002 1.0080 <br> 99 CR1 1 STY CCH 17 -0.016 12.0110 <br>
100 HC 1 STY HCH 17 0.003 1.0080 <br> 101 CR1 1 STY CCI 17 -0.016 12.0110 <br> 102 HC 1 STY HCI 17 0.003 1.0080 <br> 103 CR1 1 STY CCJ 17 -0.016 12.0110 <br>
104 HC 1 STY HCJ 17 0.003 1.0080 <br> 105 CH2 1 STY CCT 17 0.039 14.0270 <br> 106 CH1 1 STY CCS 18 0.060 13.0190 <br> 107 C 1 STY CCM 18 -0.027 12.0110 <br>
108 CR1 1 STY CCN 18 -0.018 12.0110 <br> 109 HC 1 STY HCN 18 0.001 1.0080 <br> 110 CR1 1 STY CCO 18 -0.018 12.0110 <br> 111 HC 1 STY HCO 18 0.002 1.0080 <br>
112 CR1 1 STY CCP 19 -0.016 12.0110 <br> 113 HC 1 STY HCP 19 0.003 1.0080 <br> 114 CR1 1 STY CCQ 19 -0.016 12.0110 <br> 115 HC 1 STY HCQ 19 0.003 1.0080 <br>
116 CR1 1 STY CCR 19 -0.016 12.0110 <br> 117 HC 1 STY HCR 19 0.003 1.0080 <br> 118 CH2 1 STY CDB 19 0.039 14.0270 <br> 119 CH2 1 STY CDA 20 0.066 14.0270 <br>
120 C 1 STY CCU 20 -0.019 12.0110 <br> 121 CR1 1 STY CCV 20 -0.012 12.0110 <br> 122 HC 1 STY HCV 20 0.003 1.0080 <br> 123 CR1 1 STY CCW 20 -0.013 12.0110 <br>
124 HC 1 STY HCW 20 0.004 1.0080 <br> 125 CR1 1 STY CCX 20 -0.013 12.0110 <br> 126 HC 1 STY HCX 20 0.004 1.0080 <br> 127 CR1 1 STY CCY 20 -0.013 12.0110 <br>
128 HC 1 STY HCY 20 0.003 1.0080 <br> 129 CR1 1 STY CCZ 20 -0.013 12.0110 <br> 130 HC 1 STY HCZ 20 0.003 1.0080 <br><br>[ bonds ]<br>; ai aj fu c0, c1, ...<br>
1 2 2 0.109 12300000.0 0.109 12300000.0 ; CAB HAB <br> 1 3 2 0.139 10800000.0 0.139 10800000.0 ; CAB CAC <br>.<br>.<br>.<br>.<br>.<br>************<br><br>Thank you so much for your help :)<br>
<br>Sincerely,<br>Harshith, Under Graduate,<br>IITK<br><a href="http://home.iitk.ac.in/~harshith">http://home.iitk.ac.in/~harshith</a><br>