Re: [AMBER] Methylated histidine lib and frcomd files

From: FyD <>
Date: Tue, 09 Jul 2013 15:57:53 +0200

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

> 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
>>> assigned a total charge 0 and spin multiplicity 1. But
>>> the
>>> QM optimization
>>> crashed because Firefly detected 121 electrons.
>> 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:
>>>> 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:
>>>> vs
>>>> 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 (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:
>>> 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:
>>>>>> then all together:
>>>>>> and finally all together automatically from a single dipeptide:
>>>>>> 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.
>>>>>>> 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:
>>>>>>>>> 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
>>>>>>> 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:
>>> 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:
>>>>>>>>>> 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

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Received on Tue Jul 09 2013 - 07:30:03 PDT
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