Grab data from db

[snysmumrik]

Dear all,

As an output of MOE db I get data for all conformations of molecule in a single file. Each molecule is presented like this:

<TRIPOS>MOLECULE
NONAME
28 27 1 0 0
SMALL
USER_CHARGES


@<TRIPOS>ATOM
1 C -3.2600 -0.9610 -0.1670 C.3 1 <1>
2 C -4.1980 -1.6360 0.8450 C.3 1 <1>
3 H1 -5.2480 -1.4850 0.5720 H 1 <1>
4 H2 -4.0490 -1.2270 1.8510 H 1 <1>
5 H3 -4.0270 -2.7160 0.9040 H 1 <1>
6 C -3.4170 -1.6110 -1.5490 C.3 1 <1>
7 H1 -3.2410 -2.6920 -1.5160 H 1 <1>
8 H2 -2.7040 -1.1870 -2.2660 H 1 <1>
9 H3 -4.4270 -1.4570 -1.9460 H 1 <1>
10 C -3.6360 0.5270 -0.2750 C.3 1 <1>
11 H1 -3.5390 1.0330 0.6920 H 1 <1>
12 H2 -4.6710 0.6530 -0.6150 H 1 <1>
13 H3 -2.9860 1.0500 -0.9850 H 1 <1>
14 C -1.8010 -1.0850 0.3100 C.2 1 <1>
15 O -1.0990 -0.1130 0.5820 O.2 1 <1>
16 N -1.3250 -2.3700 0.4390 N.am 1 <1>
17 H -1.9370 -3.1490 0.2390 H 1 <1>
18 C 0.0440 -2.6680 0.8420 C.3 1 <1>
19 C 0.3310 -2.3150 2.3140 C.3 1 <1>
20 H1 -0.5460 -2.5250 2.9360 H 1 <1>
21 O 0.6450 -0.9300 2.4610 O.3 1 <1>
22 H 0.0400 -0.4280 1.8700 H 1 <1>
23 C 1.5210 -3.1020 2.8440 C.3 1 <1>
24 H1 1.3360 -4.1800 2.8050 H 1 <1>
25 H2 1.7340 -2.8230 3.8820 H 1 <1>
26 H3 2.4260 -2.8800 2.2670 H 1 <1>
27 H2 0.7150 -2.1160 0.1740 H 1 <1>
28 H3 0.1770 -3.7410 0.6700 H 1 <1>

What I need for Gaussian input is to get numbers of atoms(3-rd line, 28 for this case) and get 2,3,4 columns after @<TRIPOS>ATOM - line. I realise it should be easy, but I have just started using awk, so still I am not so good in syntax. This could actually make my work easier, so I ask you to help me with finding ways to do this. Thanks.

 

[PHV]

Well, what is the expected output with the already provided input ?

Hope This Helps, PH.
FAQ219-2884
FAQ181-2886

 

[snysmumrik]

C -3.2600 -0.9610 -0.1670
C -4.1980 -1.6360 0.8450
H1 -5.2480 -1.4850 0.5720
H2 -4.0490 -1.2270 1.8510
H3 -4.0270 -2.7160 0.9040
C -3.4170 -1.6110 -1.5490
H1 -3.2410 -2.6920 -1.5160
H2 -2.7040 -1.1870 -2.2660
H3 -4.4270 -1.4570 -1.9460
C -3.6360 0.5270 -0.2750
H1 -3.5390 1.0330 0.6920
H2 -4.6710 0.6530 -0.6150
H3 -2.9860 1.0500 -0.9850
C -1.8010 -1.0850 0.3100
O -1.0990 -0.1130 0.5820
N -1.3250 -2.3700 0.4390
H -1.9370 -3.1490 0.2390
C 0.0440 -2.6680 0.8420
C 0.3310 -2.3150 2.3140
H1 -0.5460 -2.5250 2.9360
O 0.6450 -0.9300 2.4610
H 0.0400 -0.4280 1.8700
C 1.5210 -3.1020 2.8440
H1 1.3360 -4.1800 2.8050
H2 1.7340 -2.8230 3.8820
H3 2.4260 -2.8800 2.2670
H2 0.7150 -2.1160 0.1740
H3 0.1770 -3.7410 0.6700

I have already tested code like this:

BEGIN {
print("%NProcS=2")
print("%Mem=512Mb")
printf("# bhandh/6-31G* SCF=Tight \n")
printf("\n")
printf("HPMA monomer BHandH\n")
printf("\n")
printf("0 1\n")
}

/@<TRIPOS>ATOM/ {ln=NR} ln {print $2,$3,$4,$5}

END {
printf("\n")
printf("\n")
printf("\n")
}

But there are a lot of tables like this and I am now thinking on way of splitting it one from another.

 

[PHV]

But there are a lot of tables like this and I am now thinking on way of splitting it one from another.
???