VMD-L Mailing List

From: Peter Murphy (pwmurphy_at_dal.ca)
Date: Wed Apr 24 2013 - 05:52:41 CDT

Hi Josh,

    I have triple checked that the residue I am mutating is ASP not VAL.
Additionally, my protein has only one segment (only 80 amino acids in
length). I'll perhaps try without FEP (though using FEP before I was
able to use a TRP as the three letter code and it mutated fine).

Thanks for your help,

Peter

On 23/04/2013 7:49 PM, Josh Vermaas wrote:
> Hi Peter,
>
> If you are using mutator to prepare a FEP simulation, the three letter
> code won't be ASN. For FEP calculations, you want a single residue
> that has both side chains present, and to alert the user to this fact,
> the residues are given names using the one letter amino acid codes
> with a 2 indicating the direction of mutation. V2N is actually
> expected if you happen to be mutating a Valine to an Asparagine, which
> should look almost identical to ASN except for a methyl hanging off
> the mutated residue. Since you intended to mutate a ASP to ASN, the
> expected resname is actually D2N, which to me suggests you may have
> accidentally picked out the wrong residue for mutation? If your
> protein has multiple segments, you should also specify the proper
> segment name in the mutator window (ie. if the ASP you wanted to
> mutate was on segment P3 and resid 423, you'd specify the residue as
> P3:423 in the mutator GUI), and is my best guess as to why you are
> seeing unexpected results.
>
> -Josh
>
> On 04/23/2013 04:22 PM, Ajasja Ljubetič wrote:
>> Usually it's considered good form to keep the mailing list in the CC.
>>
>> I am afraid I can't help you of the top of my head. Here are some
>> generic tips:
>>
>> * Are you using the latest VMD version?
>> * Is the problem repeatable if you restart your computer
>> * Is the problem specific just for your current 3D structure or for
>> any 3D structure? (so have you tried with another pdb/psf pair?)
>>
>>
>> HTH,
>> Ajasja
>>
>>
>> On 23 April 2013 22:12, Peter Murphy <pwmurphy_at_dal.ca
>> <mailto:pwmurphy_at_dal.ca>> wrote:
>>
>> I selected the pdb and PSF files, put in the residue # and the
>> three letter code to mutate to ASN. In addition I am using FEP.
>> Not getting any error messages, the plugin says its completed fine.
>>
>> Other than that, not really anything else I can provide except
>> the input and output files (and I can if that would help).
>>
>> Thanks for your fast response... I appreciate it!!
>>
>> Peter
>>
>>
>> On 23/04/2013 4:29 PM, Ajasja Ljubetič wrote:
>>> Yes, I have two ideas:
>>>
>>> a) Describe exactly what you have done (with warning and error
>>> message) as there is not enough info in your question to help you.
>>> b) delete the surplus atoms of ASP (the oxygen and the proton),
>>> rename the residue to ASN and rebuild using psfgen.
>>>
>>> HTH,
>>> Ajasja
>>>
>>>
>>> On 23 April 2013 20:40, Peter Murphy <pwmurphy_at_dal.ca
>>> <mailto:pwmurphy_at_dal.ca>> wrote:
>>>
>>> Hello everyone,
>>>
>>> I am trying to figure out what's going on with the
>>> mutator plugin. I've used it successfully many times before
>>> (mostly for mutating to Trp), but seem to be running into
>>> problems this time around when trying to mutate to ASN.
>>> Instead of mutating ASP to ASN, it is giving my V2N?? When I
>>> turn on a CPK representation of the residue post mutation
>>> (V2N) it appears the V2N residue matches the structure of
>>> ASN almost exactly....
>>>
>>> I've run out of ideas... anyone have any thoughts?
>>>
>>> Thanks in advance,
>>>
>>> Peter
>>> --
>>> Ph.D Candidate,
>>> Dalhousie University
>>> Halifax, NS
>>> Canada
>>>
>>>
>>
>>
>