Dear users,
I have a problem related to PRODRG.
Chirality:NO
Full charges: YES
Energy minimization: NO
*İnput file name:TRS.pdb*
HETATM 1803 C TRS B 232 38.588 -4.733 65.956 1.00 17.99
C
ANISOU 1803 C TRS B 232 2126 1948 2760 -378 45 -81
C
HETATM 1804 C1 TRS B 232 40.103 -5.057 65.899 1.00 16.81
C
ANISOU 1804 C1 TRS B 232 1642 1577 3168 -531 171 120
C
HETATM 1805 C2 TRS B 232 37.795 -5.994 66.343 1.00 20.76
C
ANISOU 1805 C2 TRS B 232 2790 2021 3077 67 141 -408
C
HETATM 1806 C3 TRS B 232 38.160 -3.717 67.031 1.00 16.86
C
ANISOU 1806 C3 TRS B 232 2240 1557 2611 -491 8 -192
C
HETATM 1807 N TRS B 232 38.227 -4.154 64.652 1.00 18.26
N
ANISOU 1807 N TRS B 232 2336 2520 2083 -166 46 -112
N
HETATM 1808 O1 TRS B 232 40.741 -4.020 65.158 1.00 17.53
O
ANISOU 1808 O1 TRS B 232 1921 1579 3163 -225 147 197
O
HETATM 1809 O2 TRS B 232 37.871 -6.803 65.211 1.00 23.91
O
ANISOU 1809 O2 TRS B 232 3018 2456 3610 -48 -86 -450
O
HETATM 1810 O3 TRS B 232 38.871 -2.531 66.874 1.00 18.28
O
ANISOU 1810 O3 TRS B 232 2677 1594 2673 197 -4 -52
O
I get the output *as the following file1.itp* from your PRODRG server for
TRS ligand before 3-4 months. I think this calculate is correct:
*file1.itp*
................
[ moleculetype ]
; Name nrexcl
TRS 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OA 1 TRS O1 1 -0.240 15.9994
2 H 1 TRS HAA 1 0.052 1.0080
3 CH2 1 TRS C1 1 0.061 14.0270
4 CH1 1 TRS C 1 0.127 12.0110
5 CH2 1 TRS C3 2 0.090 14.0270
6 OA 1 TRS O3 2 -0.165 15.9994
7 H 1 TRS HAC 2 0.075 1.0080
8 NL 1 TRS N 3 0.876 14.0067
9 H 1 TRS HAE 3 0.041 1.0080
10 H 1 TRS HAF 3 0.042 1.0080
11 H 1 TRS HAD 3 0.041 1.0080
12 CH2 1 TRS C2 4 0.090 14.0270
13 OA 1 TRS O2 4 -0.165 15.9994
14 H 1 TRS HAB 4 0.075 1.0080
....................
But Now, That is, today, I get the output *as the following file2.itp* from
your PRODRG server for TRS ligand.
*file2.itp*
.....
[ moleculetype ]
; Name nrexcl
TRS 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OA 1 TRS O1 1 -0.173 15.9994
2 H 1 TRS H13 1 0.061 1.0080
3 CH2 1 TRS C1 1 0.165 14.0270
4 CCL4 1 TRS C 1 0.177 12.0110
5 CH2 1 TRS C3 1 0.165 14.0270
6 OA 1 TRS O3 1 -0.174 15.9994
7 H 1 TRS H33 1 0.062 1.0080
8 NL 1 TRS N 1 0.675 14.0067
9 H 1 TRS H2 1 0.014 1.0080
10 H 1 TRS H3 1 0.014 1.0080
11 H 1 TRS H1 1 0.014 1.0080
12 CH2 1 TRS C2 2 0.144 14.0270
13 OA 1 TRS O2 2 -0.198 15.9994
14 H 1 TRS H23 2 0.054 1.0080
....
Now, I think PRODRG calculate incorrectly cgnr charge
What should I do? can you help me?
--
Ahmet YILDIRIM
--
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