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Full Discussion: pls help
Top Forums Shell Programming and Scripting pls help Post 302123813 by chuchu on Wednesday 27th of June 2007 09:19:42 AM
Old 06-27-2007
Guys,
The two files look like this:

101.pdb looks like:

AM1 CALCULATION

LocalSCF2 1.0
Thu Nov 30 19:55:15 2006

EMPIRICAL FORMULA: C972 H1443 N254 O285 S9

AM1 1SCF CHARGE=-5 PDBINP GEO-OK USEFMM




SCF FIELD WAS ACHIEVED


HEAT OF FORMATION = -5441.095651 KCAL = -22765.54420 KJ
TOTAL ENERGY = -279587.680092 EV
ELECTRONIC ENERGY = -9120618.893231 EV
CORE-CORE REPULSION = 8841031.213139 EV
atheat = 6677719.524081 kcal
DIPOLE = 427.38051 DEBYE SYMMETRY: C1
NO. OF FILLED LEVELS = 4185
MOLECULAR WEIGHT = 21535.163
SCF CALCULATIONS = 1
COMPUTATION TIME = 381.69 SECONDS




Net atomic charges

Atom No. Type Charge No. of elecs. s-Pop p-Pop
1 N -0.050845 5.0508 1.43492 3.61592
2 H 0.270236 0.7298 0.72976
3 H 0.252319 0.7477 0.74768
4 H 0.234913 0.7651 0.76509
5 C -0.113602 4.1136 1.25325 2.86035
6 H 0.191044 0.8090 0.80896
7 C -0.168786 4.1688 1.19808 2.97071
8 H 0.091344 0.9087 0.90866
9 H 0.188577 0.8114 0.81142
10 C -0.144850 4.1449 1.18795 2.95690
11 C -0.149641 4.1496 1.20348 2.94616
12 H 0.102619 0.8974 0.89738
13 C -0.124950 4.1249 1.22177 2.90318
14 H 0.132802 0.8672 0.86720
15 C -0.092942 4.0929 1.23475 2.85819
16 H 0.164127 0.8359 0.83587
17 C -0.109979 4.1100 1.23665 2.87333
18 H 0.173796 0.8262 0.82620
19 C -0.092526 4.0925 1.23531 2.85721
20 H 0.181277 0.8187 0.81872


I have to grep the 3rd column & replace the 9th column of 101.amberized.pdb file which looks like:

ATOM 1 N PHE 1 -5.811 0.058 -26.716 0.173700 2.006 0.170 N3
ATOM 2 H1 PHE 1 -5.560 -0.954 -26.786 0.192100 0.642 0.016 H
ATOM 3 H2 PHE 1 -5.253 0.504 -27.408 0.192100 0.642 0.016 H
ATOM 4 H3 PHE 1 -6.797 0.179 -26.813 0.192100 0.642 0.016 H
ATOM 5 CA PHE 1 -5.253 0.487 -25.446 0.085900 2.042 0.109 CT
ATOM 6 HA PHE 1 -5.500 -0.259 -24.676 0.104100 1.484 0.016 H1
ATOM 7 CB PHE 1 -3.780 0.463 -25.635 -0.034300 2.042 0.109 CT
ATOM 8 HB2 PHE 1 -3.532 0.703 -26.669 0.029500 1.591 0.016 HC
ATOM 9 HB3 PHE 1 -3.387 1.233 -24.984 0.029500 1.591 0.016 HC
ATOM 10 CG PHE 1 -3.037 -0.743 -25.227 0.011800 2.042 0.086 CA
ATOM 11 CD1 PHE 1 -2.446 -1.525 -26.185 -0.125600 2.042 0.086 CA
ATOM 12 HD1 PHE 1 -2.611 -1.374 -27.225 0.133000 1.561 0.015 HA
ATOM 13 CE1 PHE 1 -1.687 -2.631 -25.813 -0.170400 2.042 0.086 CA
ATOM 14 HE1 PHE 1 -1.239 -3.154 -26.651 0.143000 1.561 0.015 HA
ATOM 15 CZ PHE 1 -1.383 -2.883 -24.442 -0.107200 2.042 0.086 CA
ATOM 16 HZ PHE 1 -0.667 -3.612 -24.038 0.129700 1.561 0.015 HA
ATOM 17 CE2 PHE 1 -2.041 -2.104 -23.470 -0.170400 2.042 0.086 CA
ATOM 18 HE2 PHE 1 -1.853 -2.350 -22.418 0.143000 1.561 0.015 HA
ATOM 19 CD2 PHE 1 -2.958 -1.089 -23.853 -0.125600 2.042 0.086 CA
ATOM 20 HD2 PHE 1 -3.486 -0.538 -23.067 0.133000 1.561 0.015 HA

Thanks for yours help. Hope now you guys can give me a concrete solution of my problem..
 

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