VMD-L Mailing List

From: Peter Murphy (pwmurphy_at_dal.ca)
Date: Wed Apr 24 2013 - 07:19:23 CDT

Not using FEP seems to work.

Thanks for your help everyone!

Peter

On 24/04/2013 7:52 AM, Peter Murphy wrote:
> 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
>>>>
>>>>
>>>
>>>
>>
>