On 2012-11-18 10:40, Atila Petrosian wrote:
Dear David
Thanks for your attention.
I have 2 problems/questions:
1) There are a specific orientation for GLN ligand with regard to protein
in my system. If I do what you said [you make a separate molecule Gln-Ala
using pymol or vmd], specific orientation for GLN ligand with regard to
protein are changed.
no since you only use the procedure for the topology creation.
2) topology obtained from NGLN-CALA is as follows:
[ moleculetype ]
; Name nrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
; residue 1 GLN rtp NGLN q +1.0
1 N3 1 GLN N 1 0.1493 14.01 ;
qtot 0.1493
2 H 1 GLN H1 2 0.1996 1.008 ;
qtot 0.3489
3 H 1 GLN H2 3 0.1996 1.008 ;
qtot 0.5485
4 H 1 GLN H3 4 0.1996 1.008 ;
qtot 0.7481
5 CT 1 GLN CA 5 0.0536 12.01 ;
qtot 0.8017
6 HP 1 GLN HA 6 0.1015 1.008 ;
qtot 0.9032
7 CT 1 GLN CB 7 0.0651 12.01 ;
qtot 0.9683
8 HC 1 GLN HB1 8 0.005 1.008 ;
qtot 0.9733
9 HC 1 GLN HB2 9 0.005 1.008 ;
qtot 0.9783
10 CT 1 GLN CG 10 -0.0903 12.01 ;
qtot 0.888
11 HC 1 GLN HG1 11 0.0331 1.008 ;
qtot 0.9211
12 HC 1 GLN HG2 12 0.0331 1.008 ;
qtot 0.9542
13 C 1 GLN CD 13 0.7354 12.01 ;
qtot 1.69
14 O 1 GLN OE1 14 -0.6133 16 ;
qtot 1.076
15 N 1 GLN NE2 15 -1.0031 14.01 ;
qtot 0.0732
16 H 1 GLN HE21 16 0.4429 1.008 ;
qtot 0.5161
17 H 1 GLN HE22 17 0.4429 1.008 ;
qtot 0.959
18 C 1 GLN C 18 0.6123 12.01 ;
qtot 1.571
19 O 1 GLN O 19 -0.5713 16 ;
qtot 1
; residue 2 ALA rtp CALA q -1.0
20 N 2 ALA N 20 -0.3821 14.01 ;
qtot 0.6179
21 H 2 ALA H 21 0.2681 1.008 ;
qtot 0.886
22 CT 2 ALA CA 22 -0.1747 12.01 ;
qtot 0.7113
23 H1 2 ALA HA 23 0.1067 1.008 ;
qtot 0.818
24 CT 2 ALA CB 24 -0.2093 12.01 ;
qtot 0.6087
25 HC 2 ALA HB1 25 0.0764 1.008 ;
qtot 0.6851
26 HC 2 ALA HB2 26 0.0764 1.008 ;
qtot 0.7615
27 HC 2 ALA HB3 27 0.0764 1.008 ;
qtot 0.8379
28 C 2 ALA C 28 0.7731 12.01 ;
qtot 1.611
29 O2 2 ALA OC1 29 -0.8055 16 ;
qtot 0.8055
30 O2 2 ALA OC2 30 -0.8055 16 ;
qtot 0
You said " Then you edit the top file (remove superfluous alanine atoms,
rename the N in ALA to O2 etc) with a text editor until it is "correct"
with help from the rtp file for CGLN. You may have to smooth the charges to
keep it neutral "
In ALA residue, all atoms except for N are redundant atoms. After removing
them and renaming N in ALA to O2, what remains in top file?
Both of NGLN and CALA or only NGLN?
If latter is true,
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
; residue 1 GLN rtp GLN q 0.0
1 N3 1 GLN N 1 0.1493 14.01 ;
qtot 0.1493
2 H 1 GLN H1 2 0.1996 1.008 ;
qtot 0.3489
3 H 1 GLN H2 3 0.1996 1.008 ;
qtot 0.5485
4 H 1 GLN H3 4 0.1996 1.008 ;
qtot 0.7481
5 CT 1 GLN CA 5 0.0536 12.01 ;
qtot 0.8017
6 HP 1 GLN HA 6 0.1015 1.008 ;
qtot 0.9032
7 CT 1 GLN CB 7 0.0651 12.01 ;
qtot 0.9683
8 HC 1 GLN HB1 8 0.005 1.008 ;
qtot 0.9733
9 HC 1 GLN HB2 9 0.005 1.008 ;
qtot 0.9783
10 CT 1 GLN CG 10 -0.0903 12.01 ;
qtot 0.888
11 HC 1 GLN HG1 11 0.0331 1.008 ;
qtot 0.9211
12 HC 1 GLN HG2 12 0.0331 1.008 ;
qtot 0.9542
13 C 1 GLN CD 13 0.7354 12.01 ;
qtot 1.69
14 O 1 GLN OE1 14 -0.6133 16 ;
qtot 1.076
15 N 1 GLN NE2 15 -1.0031 14.01 ;
qtot 0.0732
16 H 1 GLN HE21 16 0.4429 1.008 ;
qtot 0.5161
17 H 1 GLN HE22 17 0.4429 1.008 ;
qtot 0.959
18 C 1 GLN C 18 0.6123 12.01 ;
qtot 1.571
19 O2 2 GLN OC1 19 -0.8055 16 ;
qtot 0.8055
20 O2 2 GLN OC2 20 -0.8055 16 ;
qtot 0
There is not such residue in rtp file (GLN with NH3+ and CO2- terminals)
Please guide me how to resolve this problem and obtain correct topology
file.
This IS the correct topology file. Now you have to make a topology for
your protein WITHOUT ligand and then merge it in a text editor, or
better use an #include "ligand.itp"
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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