Dear all,
as requested, I'm copying here the SDS.itp file (it should be not too big):
; This file was generated by PRODRG version AA081006.0504
; PRODRG written/copyrighted by Daan van Aalten
; and Alexander Schuettelkopf
;
; Questions/comments to d...@davapc1.bioch.dundee.ac.uk
;
; When using this software in a publication, cite:
; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
; PRODRG - a tool for high-throughput crystallography
; of protein-ligand complexes.
; Acta Crystallogr. D60, 1355--1363.
[ moleculetype ]
; Name nrexcl
SDS 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OM 1 SDS O1S 1 -1.115 15.9994
2 SDMSO 1 SDS S 1 2.344 32.0600
3 OM 1 SDS O3S 1 -1.114 15.9994
4 OM 1 SDS O4 1 -1.115 15.9994
5 OA 1 SDS O2S 2 -0.211 15.9994
6 CH2 1 SDS C1 2 0.053 14.0270
7 CH2 1 SDS C12 2 0.053 14.0270
8 CH2 1 SDS C11 2 0.052 14.0270
9 CH2 1 SDS C10 2 0.053 14.0270
10 CH2 1 SDS C9 3 0.000 14.0270
11 CH2 1 SDS C8 3 0.000 14.0270
12 CH2 1 SDS C7 3 0.000 14.0270
13 CH2 1 SDS C6 3 0.000 14.0270
14 CH2 1 SDS C5 3 0.000 14.0270
15 CH2 1 SDS C4 3 0.000 14.0270
16 CH2 1 SDS C3 3 0.000 14.0270
17 CH3 1 SDS C2 4 0.000 15.0350
[ bonds ]
; ai aj fu c0, c1, ...
2 1 2 0.153 8040000.0 0.153 8040000.0 ; S O1S
2 3 2 0.153 8040000.0 0.153 8040000.0 ; S O3S
2 4 2 0.153 8040000.0 0.153 8040000.0 ; S O4
2 5 2 0.153 8040000.0 0.153 8040000.0 ; S O2S
6 5 2 0.143 8180000.0 0.143 8180000.0 ; C1 O2S
6 7 2 0.153 7150000.0 0.153 7150000.0 ; C1 C12
7 8 2 0.153 7150000.0 0.153 7150000.0 ; C12 C11
8 9 2 0.153 7150000.0 0.153 7150000.0 ; C11 C10
9 10 2 0.153 7150000.0 0.153 7150000.0 ; C10 C9
10 11 2 0.153 7150000.0 0.153 7150000.0 ; C9 C8
11 12 2 0.153 7150000.0 0.153 7150000.0 ; C8 C7
12 13 2 0.153 7150000.0 0.153 7150000.0 ; C7 C6
13 14 2 0.153 7150000.0 0.153 7150000.0 ; C6 C5
14 15 2 0.153 7150000.0 0.153 7150000.0 ; C5 C4
15 16 2 0.153 7150000.0 0.153 7150000.0 ; C4 C3
16 17 2 0.153 7150000.0 0.153 7150000.0 ; C3 C2
[ pairs ]
; ai aj fu c0, c1, ...
1 6 1 ; O1S C1
2 7 1 ; S C12
3 6 1 ; O3S C1
4 6 1 ; O4 C1
5 8 1 ; O2S C11
6 9 1 ; C1 C10
7 10 1 ; C12 C9
8 11 1 ; C11 C8
9 12 1 ; C10 C7
10 13 1 ; C9 C6
11 14 1 ; C8 C5
12 15 1 ; C7 C4
13 16 1 ; C6 C3
14 17 1 ; C5 C2
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 2 109.5 518.0 109.5 518.0 ; O1S S O3S
1 2 4 2 109.5 518.0 109.5 518.0 ; O1S S O4
1 2 5 2 109.5 518.0 109.5 518.0 ; O1S S O2S
3 2 4 2 109.5 518.0 109.5 518.0 ; O3S S O4
3 2 5 2 109.5 518.0 109.5 518.0 ; O3S S O2S
4 2 5 2 109.5 518.0 109.5 518.0 ; O4 S O2S
2 5 6 2 120.0 530.0 120.0 530.0 ; S O2S C1
5 6 7 2 109.5 520.0 109.5 520.0 ; O2S C1 C12
6 7 8 2 109.5 520.0 109.5 520.0 ; C1 C12 C11
7 8 9 2 109.5 520.0 109.5 520.0 ; C12 C11 C10
8 9 10 2 109.5 520.0 109.5 520.0 ; C11 C10 C9
9 10 11 2 109.5 520.0 109.5 520.0 ; C10 C9 C8
10 11 12 2 109.5 520.0 109.5 520.0 ; C9 C8 C7
11 12 13 2 109.5 520.0 109.5 520.0 ; C8 C7 C6
12 13 14 2 109.5 520.0 109.5 520.0 ; C7 C6 C5
13 14 15 2 109.5 520.0 109.5 520.0 ; C6 C5 C4
14 15 16 2 109.5 520.0 109.5 520.0 ; C5 C4 C3
15 16 17 2 109.5 520.0 109.5 520.0 ; C4 C3 C2
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
2 1 4 3 2 35.3 334.8 35.3 334.8 ; imp S O1S O4
O3S
1 2 5 6 1 0.0 1.3 3 0.0 1.3 3 ; dih O1S S O2S
C1
7 6 5 2 1 0.0 1.3 3 0.0 1.3 3 ; dih C12 C1 O2S
S
8 7 6 5 1 0.0 5.9 3 0.0 5.9 3 ; dih C11 C12 C1
O2S
9 8 7 6 1 0.0 5.9 3 0.0 5.9 3 ; dih C10 C11 C12
C1
10 9 8 7 1 0.0 5.9 3 0.0 5.9 3 ; dih C9 C10 C11
C12
11 10 9 8 1 0.0 5.9 3 0.0 5.9 3 ; dih C8 C9 C10
C11
12 11 10 9 1 0.0 5.9 3 0.0 5.9 3 ; dih C7 C8 C9
C10
13 12 11 10 1 0.0 5.9 3 0.0 5.9 3 ; dih C6 C7 C8
C9
14 13 12 11 1 0.0 5.9 3 0.0 5.9 3 ; dih C5 C6 C7
C8
15 14 13 12 1 0.0 5.9 3 0.0 5.9 3 ; dih C4 C5 C6
C7
16 15 14 13 1 0.0 5.9 3 0.0 5.9 3 ; dih C3 C4 C5
C6
17 16 15 14 1 0.0 5.9 3 0.0 5.9 3 ; dih C2 C3 C4
C5
...end-of-file
As I told sometimes ago, I obtained this file from PRODRG starting from a
SDS.pdb file that I created using
SDS coordinates found in another .pdb file (I simply copied and pasted the SDS
coordinates in a new file and
called it SDS.pdb). For my simulations, however, I used the SDS.gro file and
SDS.itp file generated by PRODRG.
I notice that the section [ moleculetype] is present in SDS.itp, but nothing
changes if I erase the [
moleculetype ] section for SDS in my_prot.top: in all cases it doesn't work...
I also copied and pasted the entire topology of SDS explicitly into my_prot.top
instead of typing #include
"SDS.itp", and nothing changed again...
Concerning the order of molecules in the last [ molecules ] section, I changed
it several times, and nothing
changed...
I'm still with an unclarified question: why genbox did not create by itself all
corrections necessary to the
original .top file when I used the -ci -nmol options? I added the -p flag but
it doesn't change the topology
by itself (as it should do, in my opinion).
Thank you again
Anna
______________________________________________
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science, CNR
Via Roma 64
83100 Avellino (Italy)
Phone: +39 0825 299651
Fax: +39 0825 781585
Skype: annam1972
E-mail: amarabo...@isa.cnr.it
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
____________________________________________________
"If you think you are too small to make a difference, try sleeping with a
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