ahmet yıldırım wrote:
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
I agree with Tsjerk that you should contact the PRODRG developers regarding the
differences, but I would also say that neither of these files is correct.
PRODRG has never given reliable charges. See, for instance (something I posted
dozens of times before):
http://pubs.acs.org/doi/abs/10.1021/ci100335w
-Justin
What should I do? can you help me?
--
Ahmet YILDIRIM
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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