> First one
> is the blank lines in the resp input file. I have
> followed the same
> procedure for adenosine and DMP. I have created the
> .dat file and the 1st
> and 2nd resp.in files. But I did not understand the
> blank lines. In your
> sample file, u dont use the 7th area, so u have a
> blank line there. Let me
> copy/past those parts:
> ----------------
> .
> .
> 1 0
> 1 0
>
> 6 0.000
> 1 6 1 14 2 2 2 3 2 4
> 2 5
> 6 0.000
> 1 1 1 9 2 10 2 11 2 12
> 2 13
>
>
>
>
> --------------
> Then, u have described the intermolecular charge
> constraints. After that
> you have 4 blank lines. This is for the 1st resp
> fit. Why do you have 4
> blank lines but not just 1? On the second fit, you
> have 7 blank lines
> after the 6th area (no inter/intramolecular charge
> constraints and
> multiple molecule atom equivalencing is used). How
> should someone decide
> how many blank lines to use?
This is a tricky part of setting up RESP runs. The
RESP manual says "*blank to end" after the 7th, 8th,
or 9th area, but it does not say how many blank lines
should be given before the end of the file. So I
tested and found that there should be at least three
blank lines before the end to make RESP work
correctly. Therefore, I added three or more than three
blank lines before the end. Sorry, I should have
included explanation in the sample. Thanks for asking,
and I just updated the readme file in the sample.
> My 2nd question is about the perl scripts u provide
> in your sample. My
> question is about the 'p_d_q2q.pl' file. The program
> needs some files in
> order to convert the resp output files to an AMBER
> file. Here is the
> command line for this script:
> # -----------------------------------------
> # To run, type: perl p_d_q2q.pl -p abc.pdb [-p2
> abc2.pdb] -q abc.pch -d
> # abc.in -o charges.dat
> # -- abc.pdb: abc's PDB file
> # -- abc2.pdb: second PDB file, if abc.pdb and
> abc2.pdb produce abc.pch
> # together AND
> # abc2.pdb produces the 2nd part of
> abc.pch
> # -- abc.pch: charges output file from RESP
> # -- abc.in: abc's AMBER database file
> # -- charges.dat: charges in the order and format of
> database file
> #
> # Qing Zhang, Dept. of Chemistry, New York
> University
> # May. 16, 2002 (freeware, no warranty)
> #
> # -----------------------------
>
> If we use 2 files (as it is done in the sample) we
> have to provide both of
> these .pdb files in the command line as -p and -p2.
> -q is just the .pch
> output of the resp procedure. I did not understand
> what is meant by -d and
> -o and how to get those files.
The option -d is followed by the ABMER database file (
PREP input file) "abc.in" you built for your new
residue "abc", which is not in the AMBER force field.
The file will be loaded to LEaP with the command
"loadAmberPrep". A sample of the file is at the end of
this email. However, the file has no partial charges
yet. So with the above Perl program, you can convert
the RESP output charges to the format and order in
your database file. The converted partial charges are
saved in "charges.dat" that followes the "-o" option.
Sincerely,
Qing
=========== abc.in (without charges) ===========
1 0 2
dac.db94
D-ADENOSINE - DA with carcinogen (general, no charges)
DAC INT 1
CORRECT OMIT DU BEG
0.0
1 DUMM DU M 0 -1 -2
2 DUMM DU M 1 0 -1
3 DUMM DU M 2 1 0
4 P P M 3 2 1
5 O1P O2 E 4 3 2
6 O2P O2 E 4 3 2
7 O5' OS M 4 3 2
8 C5' CT M 7 4 3
9 H5'1 H1 E 8 7 4
10 H5'2 H1 E 8 7 4
11 C4' CT M 8 7 4
12 H4' H1 E 11 8 7
13 O4' OS S 11 8 7
14 C1' CT B 13 11 8
15 H1' H2 E 14 13 11
16 N9 N* B 14 13 11
17 C8 CK S 16 14 13
18 H8 H5 E 17 16 14
19 C4 CB B 16 14 13
20 N3 NC E 19 16 14
21 C5 CB B 19 16 14
22 N7 NB E 21 19 16
23 C6 CA B 21 19 16
24 N1 NC S 23 21 19
25 C2 CQ S 24 23 21
26 H2 H5 E 25 24 23
27 N6 N2 B 23 21 19
28 H6 H E 27 23 21
29 CC1 CT B 27 23 21
30 HC1 H1 E 29 27 23
31 CC2 CT 3 29 27 23
32 HC2 H1 E 31 29 27
33 O9 OH S 31 29 27
34 HO9 HO E 33 31 29
35 CC3 CT 3 31 29 27
36 HC3 H1 E 35 31 29
37 O8 OH S 35 31 29
38 HO8 HO E 37 35 31
39 CC4 CT 3 35 31 29
40 HC4 H1 E 39 35 31
41 O7 OH S 39 35 31
42 HO7 HO E 41 39 35
43 CC5 CA S 39 35 31
44 CC6 CA B 43 39 35
45 HC6 HA E 44 43 39
46 CC7 CA B 44 43 39
47 C20 CA E 46 44 43
48 CC8 CA B 46 44 43
49 HC8 HA E 48 46 44
50 CC9 CA B 48 46 44
51 HC9 HA E 50 48 46
52 C10 CA B 50 48 46
53 C19 CA E 52 50 48
54 C11 CA B 52 50 48
55 HC11 HA E 54 52 50
56 C12 CA B 54 52 50
57 HC12 HA E 56 54 52
58 C13 CA B 56 54 52
59 HC13 HA E 58 56 54
60 C14 CA S 58 56 54
61 C15 CA B 60 58 56
62 HC15 HA E 61 60 58
63 C16 CA B 61 60 58
64 HC16 HA E 63 61 60
65 C17 CA S 63 61 60
66 C18 CA E 65 63 61
67 C3' CT M 11 8 7
68 H3' H1 E 67 11 8
69 C2' CT B 67 11 8
70 H2'1 HC E 69 67 11
71 H2'2 HC E 69 67 11
72 O3' OS M 67 11 8
CHARGE deoxy -resp charges A
IMPROPER
LOOP CLOSING EXPLICIT
C2' C1'
N7 C8
C2 N3
C18 CC1
C18 CC5
C17 C20
C19 C20
C14 C19
DONE
STOP
===============================
____________________________________________________
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Received on Tue Jul 12 2005 - 21:53:01 PDT
