Dear All,I have sketched my ligand via chem draw then minimize it via MOE run docking. After docking I have prepared topology files of my ligand using antechamber then I check my structure on xleap after loading prepin and frcmod it is perfectly fine and all iodine atoms are connected with benzene moiety, but the problem is when I visualize this NEWPDB.PDb file on vmd, it shows broken iodine bond. I have pasted my NEWPDB.PDB file with frcmod and prepin below.> NEWPDB
ATOM 1 C LIG 1 -5.645 -11.299 8.597 -0.014200
ATOM 2 C1 LIG 1 -6.557 -10.878 7.605 0.053900
ATOM 3 I LIG 1 -8.291 -9.807 8.174 -0.097900
ATOM 4 C3 LIG 1 -6.364 -11.375 6.280 0.075900
ATOM 5 I1 LIG 1 -7.480 -10.500 4.647 -0.085900
ATOM 6 C4 LIG 1 -5.466 -12.439 6.024 0.040900
ATOM 7 I2 LIG 1 -5.178 -13.233 4.028 -0.085900
ATOM 8 C5 LIG 1 -4.764 -13.020 7.098 0.112900
ATOM 9 I3 LIG 1 -3.743 -14.874 6.988 -0.076900
ATOM 10 C6 LIG 1 -4.789 -12.379 8.357 0.096400
ATOM 11 N LIG 1 -4.070 -12.693 9.482 -0.546100
ATOM 12 C7 LIG 1 -4.394 -11.792 10.370 0.434700
ATOM 13 H7 LIG 1 -4.010 -11.739 11.236 0.074800
ATOM 14 N1 LIG 1 -5.351 -10.934 9.906 -0.183300
ATOM 15 C10 LIG 1 -5.893 -9.847 10.710 0.233800
ATOM 16 C9 LIG 1 -6.995 -10.289 11.669 -0.114400
ATOM 17 C8 LIG 1 -6.300 -10.307 13.012 0.122100
ATOM 18 O LIG 1 -7.204 -10.145 14.086 -0.585800
ATOM 19 H LIG 1 -6.722 -10.162 14.916 0.414000
ATOM 20 H8 LIG 1 -5.815 -11.116 13.115 0.059700
ATOM 21 H92 LIG 1 -7.715 -9.671 11.667 0.097700
ATOM 22 H93 LIG 1 -7.303 -11.158 11.443 0.079700
ATOM 23 H10 LIG 1 -6.239 -9.180 10.131 0.119700
ATOM 24 O1 LIG 1 -4.843 -9.266 11.518 -0.404600
ATOM 25 C11 LIG 1 -5.340 -9.142 12.862 0.057100
ATOM 26 H11 LIG 1 -5.817 -8.326 12.949 0.081700
ATOM 27 C2 LIG 1 -4.187 -9.164 13.852 0.108400
ATOM 28 H22 LIG 1 -4.521 -9.352 14.720 0.069700
ATOM 29 H23 LIG 1 -3.567 -9.837 13.600 0.056700
ATOM 30 O23 LIG 1 -3.535 -7.898 13.860 -0.596800
ATOM 31 H231LIG 1 -2.808 -7.916 14.486 0.404000
> prepin file
0 0 2
This is a remark line
molecule.res
LIG XYZ 0
CHANGE OMIT DU BEG
0.0000
1 DUMM DU M 999.000 999.0 -999.0 .00000
2 DUMM DU M 999.000 -999.0 999.0 .00000
3 DUMM DU M -999.000 999.0 999.0 .00000
4 C ca M -5.645000 -11.299000 8.597000 -0.014200
5 C1 ca M -6.557000 -10.878000 7.605000 0.053900
6 I i E -8.291000 -9.807000 8.174000 -0.097900
7 C3 ca M -6.364000 -11.375000 6.280000 0.075900
8 I1 i E -7.480000 -10.500000 4.647000 -0.085900
9 C4 ca M -5.466000 -12.439000 6.024000 0.040900
10 I2 i E -5.178000 -13.233000 4.028000 -0.085900
11 C5 ca M -4.764000 -13.020000 7.098000 0.112900
12 I3 i E -3.743000 -14.874000 6.988000 -0.076900
13 C6 ca M -4.789000 -12.379000 8.357000 0.096400
14 N nc M -4.070000 -12.693000 9.482000 -0.546100
15 C7 cd M -4.394000 -11.792000 10.370000 0.434700
16 H7 h5 E -4.010000 -11.739000 11.236000 0.074800
17 N1 na M -5.351000 -10.934000 9.906000 -0.183300
18 C10 c3 M -5.893000 -9.847000 10.710000 0.233800
19 C9 c3 3 -6.995000 -10.289000 11.669000 -0.114400
20 C8 c3 B -6.300000 -10.307000 13.012000 0.122100
21 O oh S -7.204000 -10.145000 14.086000 -0.585800
22 H ho E -6.722000 -10.162000 14.916000 0.414000
23 H8 h1 E -5.815000 -11.116000 13.115000 0.059700
24 H92 hc E -7.715000 -9.671000 11.667000 0.097700
25 H93 hc E -7.303000 -11.158000 11.443000 0.079700
26 H10 h2 E -6.239000 -9.180000 10.131000 0.119700
27 O1 os M -4.843000 -9.266000 11.518000 -0.404600
28 C11 c3 M -5.340000 -9.142000 12.862000 0.057100
29 H11 h1 E -5.817000 -8.326000 12.949000 0.081700
30 C2 c3 M -4.187000 -9.164000 13.852000 0.108400
31 H22 h1 E -4.521000 -9.352000 14.720000 0.069700
32 H23 h1 E -3.567000 -9.837000 13.600000 0.056700
33 O23 oh M -3.535000 -7.898000 13.860000 -0.596800
34 H231 ho E -2.808000 -7.916000 14.486000 0.404000
LOOP
C6 C
N1 C
C11 C8
IMPROPER
C6 C1 C N1
C C3 C1 I
C1 C4 C3 I1
C5 C3 C4 I2
C6 C4 C5 I3
C5 C C6 N
H7 N1 C7 N
C10 C N1 C7
DONE
STOP
> frcmodremark goes here
MASS
BOND
ANGLE
DIHE
IMPROPER
ca-ca-ca-na 1.1 180.0 2.0 Using default value
ca-ca-ca-nc 1.1 180.0 2.0 Using default value
h5-na-cd-nc 1.1 180.0 2.0 Using default value
c3-ca-na-cd 1.1 180.0 2.0 Using default value
NONBON
I would greatly appreciate it if anyone help me in this regard.
Thank you.
Best Regards, Saman Yousuf AliJunior Research Fellow,
| Lab No. P-133, Computational Chemistry Laboratory
Dr. Panjwani Center for Molecular Medicine & Drug Research,
International Center for Chemical & Biological Sciences,
University of Karachi – 75270.Karachi-Pakistan.
Contact No:
Office (92-21) 111222292 (Ext 309)
Email ID: saman.yousufali64.yahoo.com
saman.ali.iccs.edu
|
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Received on Fri Feb 12 2016 - 23:00:04 PST
