Quoting George Patargias <gpat.bioacademy.gr>:
> 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.
ups sorry George - you are right; you used the public account and
obviously nobody (but the admin) can kill a job executed in the public
account...
See
http://q4md-forcefieldtools.org/REDS/faq.php#10
ok - I will kill this P5748 job... I checked, Yes, You are the author
of the P5748 job ;-)
Using a private account at R.E.D. Server provides more features...
See
http://q4md-forcefieldtools.org/REDS/faq.php#3
regards, Francois
>> 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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Received on Tue Jul 09 2013 - 07:30:05 PDT
