Re: [AMBER] error in MD of modeled & docked protein - DAN complex

From: Sangita Kachhap <>
Date: Fri, 17 Dec 2010 21:57:34 +0530 (IST)

Thanks for reply

But I have already done it. I have added TER card between two strand as well
as change the name of second strand of DNA B to C.

When I load it in tleap giving error that:
> mol = loadpdb cluster3_1.pdb
Loading PDB file: ./cluster3_1.pdb
Created a new atom named: P within residue: .R<DC5 108>
Created a new atom named: O1P within residue: .R<DC5 108>
Created a new atom named: O2P within residue: .R<DC5 108>

These atoms were added by HADDOCK before docking these atoms were not there.
And the above CYT is CYT 21 but tleap reading it CYT 108, in my PDB there is
1-87 protein
1-20 DNA first strand 21-40 DNA second strand.

so please sugest me any solution.

> On Thu, Dec 16, 2010, Sangita Kachhap wrote:
>> When I checked the PDB generated after docking TER card was removed
>> between two DNA strand and both strand were of same chain name.
>> so I think these are the reasons for bonding of two strand during
>> minimization.
>> So can anybody sugest me how to resolve this.
> Edit the pdb file created by Haddock and put in the proper TER cards.
> ....dac
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Sangita Kachhap

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Received on Fri Dec 17 2010 - 08:30:08 PST
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