Dear Francois
Many thanks for your comments; they are indeed very helpful!
Could you please kill my P5748 job on the R.E.D server? It has the
wrong total charge and multiplicity. I tried to do it myself with the
login/password I just created but I couldn't. Maybe because I submitted
the job before creating the login details.
Regards
George
> Dear George,
>
> Please, do not write directly to me, but to the q4md-fft or Amber
> mailing list.
>
>> I created the correct dipeptide as you said (attached). The
>> Ante_RED-1.5.pl assigned a total charge 0 and spin multiplicity 1. But
>> the
>> QM optimization
>>
>> crashed because Firefly detected 121 electrons.
>>
>> *** CHECK YOUR INPUT CHARGE AND MULTIPLICITY ***
>> THERE ARE 121 ELECTRONS, WITH CHARGE ICHARG= 0
>
> I look at your P2N file; this is far better...
> Howver by now the total charge of your HIC residue = 1; indeed you
> have generated a N-methylated imidazole ring with a N-H group; so the
> total charge = +1.
>
>> I think that total charge 0 is correct - I have a HID type of histidine.
>> But how should I check for the multiplicity?
>
> - For the ground state of organic molecules the spin multiplicity = 1.
>
> - For bio-inorganic complex the spin multiplicity = 'the number of
> single electron' + 1.
>
> Let's take an example:
> 3d10 4s1
> Copper Cu 29 (11) [Ar].3d10.4s1 || || || || || |
> 3d10
> -> Cu+ 28 (10) [Ar].3d10 || || || || ||
> -> 0 single electron
> -> spin multiplicity = 1
> 3d9
> -> Cu++ 27 (9) [Ar].3d9 || || || || |
> -> 1 single electron
> -> spin multiplicity = 1+1 = 2
>
> i hope this helps...
>
> regards, Francois
>
>
>>> 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
>
>
>
> _______________________________________________
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>
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 Tue Jul 09 2013 - 07:00:02 PDT
