Re: [AMBER] disulfide bond warnings

From: George Tzotzos <gtzotzos.me.com>
Date: Wed, 21 Mar 2012 00:19:41 +0100

HI Jason,

Numerically, they seem to be way out. Disulfide bonds are ~2 . Tleap has a cutoff of 2.2 (see AmberTools "disulfcut"). I was wondering if it is appropriate to use - if possible at all - tleap to adjust the bond length to this cutoff distance. But even if it were, wouldn't this create "distortions" elsewhere?

As I mentioned earlier the starting structure was generated by homology modelling.

Thanking you for your suggestions

George

On Mar 21, 2012, at 12:01 AM, Jason Swails wrote:

> On Tue, Mar 20, 2012 at 2:30 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> Hi everybody,
>>
>> In building a topology file, I get the following disulfide bond warnings:
>>
>> Checking Unit.
>> WARNING: There is a bond of 3.493686 angstroms between:
>> ------- .R<CYX 19>.A<SG 8> and .R<CYX 54>.A<SG 8>
>> WARNING: There is a bond of 3.201259 angstroms between:
>> ------- .R<CYX 50>.A<SG 8> and .R<CYX 108>.A<SG 8>
>> WARNING: There is a bond of 3.240445 angstroms between:
>> ------- .R<CYX 97>.A<SG 8> and .R<CYX 117>.A<SG 8>
>> WARNING: The unperturbed charge of the unit: -8.998000 is not zero.
>>
>> Is it safe to disregards them?
>>
>
> Are any of them unexpected to you? (Visualizing is typically very helpful
> with this)
>
> If they are not unexpected, these are fine.
>
> HTH,
> Jason
>
>
>>
>> Note that the original pdb file was built by means of homology modelling.
>>
>> Many thanks for any suggestions
>>
>> George
>>
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>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Mar 20 2012 - 16:30:04 PDT
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