Hi Saman,
What do you expect to get from seeing a bond in the pdb?
You could manually add a CONECT record to the pdb so that display
programs would display it ok.
Bill
On 2/12/16 11:04 PM, Saman Yousuf ali wrote:
> Dear Bill,
> Thank you for your prompt and kind response. As you recommended me, I did the same. I have loaded prmtop and NEWPDB.PDB file on vmd then it shows all connection of iodine atoms. But my question is why it is not showing connection of iodine atoms with out loading prmtop file. I want connected iodine atoms in NEWPDB.PDB for any other purpose. Kindly 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
>
> |
>
>
>
> On Saturday, February 13, 2016 11:48 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>
> If vmd will take a prmtop as input, that would tell it to draw the bond.
>
> Bill
>
> On 2/12/16 10:30 PM, Saman Yousuf ali wrote:
>> 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 Sat Feb 13 2016 - 12:00:03 PST
