Dear Francois
The RED job P5749 with the methyl-histidine dipeptide has finished.
Would it be possible to post-process the R.E.D. Server/R.E.D. IV data to
generate atom types, residue connections and frcmod files?
Thanks
George
> Dear George,
>
> You first need to create a _correct_ dipeptide molecule, and then save
> it to the PDB file format; ACE means CH3CO & NME means NHCH3 (at that
> time you will be able to run Ante_R.E.D. (better using ante_R.E.D. 2.0
> vs 1.x; in your case 1.x should be ok).
>
> in your case you need to create:
> CH3CO-NHCH(R)CO-NHCH3 i.e. ACE-HIC-NME
> R = side chain of this methylated residue
> (it looks like yours has a total charge = 0)
> pay attention to:
> - create two trans peptide bonds
> - define the phi, psi & chi dihedral angles...
>
> then carefully read:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
> vs
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
> and it should be OK ;-)
>
> we can post-process your R.E.D. Server/R.E.D. IV data using R.E.D.
> Python so that the atom types, residue connections and frcmod files
> are automatically generated; just ask in the q4md-fft or Amber list
> and provide the PXXXX R.E.D. Server job name... R.E.D. Python handles
> by now all the Amber XX force fields (XX = year).
>
> regards, Francois
>
>
>
>> I created a pdb with a methylated His together with ACE and NMA caps
>> (attached). Then I run Ante_RED-1.5.pl (from the RED-III.52-Tools) on
>> this pdb to create a p2n file (attached).
>>
>> The R.E.D. Server/Ante_R.E.D. 2.0 generates a p2n file with only one
>> residue
>> which I guess is what is needed in this case.
>>
>> Finally, I went to the R.E.D server, I selected the "Use RED IV for
>> automatically generating amino acid fragments" option and I uploaded
>> the attached p2n file. Thie job crashed with the error in the log file:
>>
>> ERROR: Wrong inter-molecular charge constraint or equivalencing
>
>>> Dear George,
>>>
>>>> It sounds like it is a lot easier if I use the R.E.D server where the
>>>> work-flow has been automated, right?
>>>
>>> you first run R.E.D. Server/Ante_R.E.D. 2.0 & then re-run R.E.D.
>>> Server/R.E.D. IV after having checked/modified (if needed) the p2n
>>> file generated by Ante_R.E.D.
>>>
>>> PDB --> P2N ---> mol2
>>> please see: http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#1
>>>
>>> We are aware these 2 steps are a limiting factor by now; the main
>>> advantage is that the user can modify the P2N file(s) after its
>>> generation and this makes the system quite flexible and allows
>>> handling complex cases of charge derivation
>>>
>>> With R.E.D. python all is combined in one step. But in this case the
>>> code is far more 'sophisticated'.
>>>
>>>> I saw that the server interfaces either with Ante_R.E.D. 2.0 or
>>>> R.E.D.
>>>> IV
>>>> program. Can you tell me what is the difference and which one should I
>>>> use?
>>>
>>> Please read the tutorials; in short you first execute Ante_R.E.D. to
>>> generate the P2N file(s) using PDB file(s) as input and then using the
>>> P2N file(s) you execute RED in a second step
>>>
>>>> Just to double check: is this approach suitable for a methyl-histidine
>>>> residue that is a part of a protein (actin)? I will extract this
>>>> residur
>>>> from the original pdb file and then upload it to the server.
>>>
>>> You extract this residue from the protein (or you construct it by
>>> controlling the conformation i.e. the phi, psi and chi dihedrals),
>>> transform it into a dipeptide (PDB file to be transformed into P2N
>>> file) and then from this dipeptide you generate the central (and
>>> N-term & C-term) fragments (to be re-inserted in your protein) using
>>> R.E.D. Server/R.E.D.
>>>
>>> See:
>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#16
>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#17
>>> then all together:
>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
>>> and finally all together automatically from a single dipeptide:
>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
>>>
>>> regards, Francois
>>>
>>>
>>>> Dear George,
>>>>
>>>>> Does R.E.D. III.x need a GAMESS installation which the perl script
>>>>> will
>>>> somehow locate?
>>>>
>>>> See the installation procedure described in the RED version II pdf
>>>> file.
>>>> http://q4md-forcefieldtools.org/RED/RED-II.pdf
>>>> See the part "-III- HOW TO USE R.E.D. & X R.E.D.?" page 9
>>>>
>>>> i.e. you need to:
>>>> - Install GAMESS (or Firefly or Gaussian) _and_ RESP.
>>>> - Check that GAMESS (Firefly or Gaussian) works from your X-terminal.
>>>> (i.e. the binaries and scratch path are defined and found)
>>>> - Same remark for RESP: install & test it before interfacing it with
>>>> R.E.D.
>>>> you can use the standalone version of the RESP program from our web
>>>> site:
>>>> http://q4md-forcefieldtools.org/RED/resp/
>>>>
>>>>>> From R.E.D. III.x, we obtain a Tripos mol2 file that we can directly
>>>> then
>>>>> load into leap and get the .lib and .frcmod files we want?
>>>>> After loading the mol2 file into leap, do we need to run some kind of
>>>> script to change atomnames etc?
>>>>
>>>> If you use R.E.D. Server/Ante_R.E.D. 2.0 atom names are checked (i.e.
>>>> in
>>>> the philosophy of a FF library two atoms can NOT share the same name
>>>> in
>>>> a given residue). See
>>>> http://q4md-forcefieldtools.org/REDS/news.php#2
>>>>
>>>> Once you got the mol2 file(s) from R.E.D. perl you need to add the FF
>>>> atom types; here we do use a LEaP script and define eaxh FF atom types
>>>> using the 'set' command.
>>>> See for instance:
>>>> http://q4md-forcefieldtools.org/REDDB/Projects/W-46/
>>>> http://q4md-forcefieldtools.org/REDDB/Projects/W-46/script1.ff
>>>>
>>>> regards, Francois
>>>>
>>>> PS With R.E.D. Python all is done automatically from a PDB file.
>>>>
>>>>
>>>>>> Dear George,
>>>>>>> I was wondering if any user has constructed a lib/prep and a frcmod
>>>>> file
>>>>>>> for a methylated histidine to share with me.
>>>>>>> If no, what is the general procedure to make these files?
>>>>>>>> From the tutorial:
>>>>> http://ambermd.org/tutorials/advanced/tutorial1_adv/
>>>>>>> I understand that a RESP calculation must be made with R.E.D to get
>>>> the
>>>>> partial charges.
>>>>>>> Then, I think some AmberTools must be used but I am not sure which.
>>>>>> See Figure 1 at
>>>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#0
>>>
>
>
>
Dr. George Patargias
Postdoctoral Researcher
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece
Office: +302106597568
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Received on Wed Jul 10 2013 - 00:30:02 PDT
