[gmx-users] regarding ligands in proteins
Luke Czapla
czapla at rutchem.rutgers.edu
Wed Oct 24 22:48:37 CEST 2001
Hi David,
I pdb2gmx-ed the glucose molecule replacing it as GLCA. This worked
very well, the only odd thing I noticed was that the total charge of the
system went from -4.0 (which is what it is supposed to be) to -5.1. I
can't explain this. I used the ffgmx force field.
You are probably correct about the PRODRG output. However, we think the
charges are fairly strange. They do not match well with the ffgmx
charges in the rtp file. And if these are similar to GROMOS87 values,
there is a big difference here. Here's the PRODRG output as an
attachment. We very much like the PRODRG server so being able to
interpret its output is important to us (because not everything has an RTP
entry).
cheers,
Luke
On Wed, 24 Oct 2001, David van der Spoel wrote:
> this is due to the different definition of the bond potential in gromos96
> and gromos87 force field (what PRODRG generates when you select gromacs).
> The conversion formulas are in the gromacs manual.
>
> How about pdb2gmx-ing the renamed glucose molecule?
>
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576, 75123 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
-------------- next part --------------
[ moleculetype ]
;name nrexcl
GLC 3
;
;
; This file was generated by PRODRG version 050901
; PRODRG written/copyrighted by Daan van Aalten
;
; Questions/comments to dava at davapc1.bioch.dundee.ac.uk
;
; When using this software in a publication, cite:
; D.M.F. van Aalten, R. Bywater, J.B.C. Findlay,
; M. Hendlich, R.W.W. Hooft and G. Vriend,
; PRODRG, a program for generating molecular topologies
; and unique molecular descriptors from coordinates
; of small molecules.
; Journal of Computer Aided Molecular Design (1996), 10, 255-262.
;
;
[ atoms ]
; nr type resnr resid atom cgnr charge
1 H 1 GLC HD 1 0.000
2 OA 1 GLC O4 2 0.000
3 CH1 1 GLC C4 3 0.000
4 CH1 1 GLC C3 4 0.150
5 OA 1 GLC O3 4 -0.548
6 H 1 GLC HC 4 0.398
7 CH1 1 GLC C2 5 0.150
8 OA 1 GLC O2 5 -0.548
9 H 1 GLC HB 5 0.398
10 CH1 1 GLC C1 6 0.150
11 OA 1 GLC O1 6 -0.548
12 H 1 GLC HA 6 0.398
13 O 1 GLC O5 7 0.000
14 CH1 1 GLC C5 8 0.000
15 CH2 1 GLC C6 9 0.150
16 OA 1 GLC O6 9 -0.548
17 H 1 GLC HE 9 0.398
[ bonds ]
;ai aj fu c0 c1
1 2 1 0.100 750.0 ; HD O4
2 3 1 0.143 800.0 ; O4 C4
3 4 1 0.153 800.0 ; C4 C3
3 14 1 0.153 800.0 ; C4 C5
4 5 1 0.143 800.0 ; C3 O3
4 7 1 0.153 800.0 ; C3 C2
5 6 1 0.100 750.0 ; O3 HC
7 8 1 0.143 800.0 ; C2 O2
7 10 1 0.153 800.0 ; C2 C1
8 9 1 0.100 750.0 ; O2 HB
10 11 1 0.143 600.0 ; C1 O1
10 13 1 0.144 600.0 ; C1 O5
11 12 1 0.100 750.0 ; O1 HA
13 14 1 0.144 600.0 ; O5 C5
14 15 1 0.153 600.0 ; C5 C6
15 16 1 0.143 800.0 ; C6 O6
16 17 1 0.100 750.0 ; O6 HE
[ pairs ]
;ai aj fu c0 c1
1 4 1 ; HD O4
1 14 1 ; HD O4
2 5 1 ; O4 C4
2 7 1 ; O4 C4
2 13 1 ; O4 C4
2 15 1 ; O4 C4
3 6 1 ; C4 C3
3 8 1 ; C4 C3
3 10 1 ; C4 C3
3 16 1 ; C4 C3
4 9 1 ; C4 C5
4 11 1 ; C4 C5
4 13 1 ; C4 C5
4 15 1 ; C4 C5
5 8 1 ; C3 O3
5 10 1 ; C3 O3
5 14 1 ; C3 O3
6 7 1 ; C3 C2
7 12 1 ; O3 HC
7 14 1 ; O3 HC
8 11 1 ; C2 O2
8 13 1 ; C2 O2
9 10 1 ; C2 C1
10 15 1 ; O2 HB
11 14 1 ; C1 O1
12 13 1 ; C1 O5
13 16 1 ; O1 HA
14 17 1 ; O5 C5
[ angles ]
;ai aj ak fu c0 c1
1 2 3 1 109.5 95.0 ; HD O4 C4
2 3 4 1 109.5 110.0 ; O4 C4 C3
2 3 14 1 109.5 110.0 ; O4 C4 C5
4 3 14 1 111.0 110.0 ; C3 C4 C5
3 4 5 1 109.5 110.0 ; C4 C3 O3
3 4 7 1 111.0 110.0 ; C4 C3 C2
5 4 7 1 109.5 110.0 ; O3 C3 C2
4 5 6 1 109.5 95.0 ; C3 O3 HC
4 7 8 1 109.5 110.0 ; C3 C2 O2
4 7 10 1 111.0 110.0 ; C3 C2 C1
8 7 10 1 109.5 110.0 ; O2 C2 C1
7 8 9 1 109.5 95.0 ; C2 O2 HB
7 10 11 1 109.5 68.0 ; C2 C1 O1
7 10 13 1 109.5 68.0 ; C2 C1 O5
11 10 13 1 109.5 68.0 ; O1 C1 O5
10 11 12 1 109.5 95.0 ; C1 O1 HA
10 13 14 1 109.5 80.0 ; C1 O5 C5
3 14 13 1 109.5 68.0 ; C4 C5 O5
3 14 15 1 109.5 60.0 ; C4 C5 C6
13 14 15 1 109.5 68.0 ; O5 C5 C6
14 15 16 1 109.5 110.0 ; C5 C6 O6
15 16 17 1 109.5 95.0 ; C6 O6 HE
[ dihedrals ]
;ai aj ak al fu c0 c1 m
3 2 14 4 2 35.3 20.0 0 ; IDI C4 O4 C5 C3
4 3 5 7 2 35.3 20.0 0 ; IDI C3 C4 O3 C2
7 4 10 8 2 35.3 20.0 0 ; IDI C2 C3 C1 O2
10 7 11 13 2 35.3 20.0 0 ; IDI C1 C2 O1 O5
14 3 13 15 2 35.3 20.0 0 ; IDI C5 C4 O5 C6
14 3 2 1 1 0.0 0.3 3 ; DI C5 C4 O4 HD
7 4 3 2 1 0.0 1.4 3 ; DI C2 C3 C4 O4
2 3 14 15 1 0.0 1.4 3 ; DI O4 C4 C5 C6
3 4 5 6 1 0.0 0.3 3 ; DI C4 C3 O3 HC
10 7 4 3 1 0.0 1.4 3 ; DI C1 C2 C3 C4
4 7 8 9 1 0.0 0.3 3 ; DI C3 C2 O2 HB
4 7 10 13 1 0.0 1.4 3 ; DI C3 C2 C1 O5
7 10 11 12 1 0.0 0.3 3 ; DI C2 C1 O1 HA
7 10 13 14 1 0.0 0.9 3 ; DI C2 C1 O5 C5
15 14 13 10 1 0.0 0.9 3 ; DI C6 C5 O5 C1
3 14 15 16 1 0.0 1.4 3 ; DI C4 C5 C6 O6
14 15 16 17 1 0.0 0.3 3 ; DI C5 C6 O6 HE
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