Hello Francois
I still cannot do it. I get the following message after I enter
login/password and job id
JOB DELETION
The R.E.D. Server job with the JOB NAME "P5748" was not deleted.
This likely means the R.E.D. Server JOB NAME provided is not correct, or
you do not have the rights to kill this job.
George
> Dear George,
>
>> Could you please kill my P5748 job on the R.E.D server?
>
> Please try; it should work... If it does not work, yes, i will kill
> your job...
> simply provide your login (i.e. the email you used to register)
> the password you received by email
> and P5748 as the R.E.D. Server job name
>
> http://cluster.q4md-forcefieldtools.org/qstat/qstat.php
> http://q4md-forcefieldtools.org/REDS/delete-log.php
>
>> 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.
>
> I just ran a job for a user to test a problem he encountered. I kikked
> my job without any problem...
>
> regards, Francois
>
>
>>> 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 - 07:30:04 PDT
