Re: [AMBER] Methylated histidine lib and frcomd files

From: FyD <>
Date: Sun, 07 Jul 2013 17:50:28 +0200

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:
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 Sun Jul 07 2013 - 09:00:03 PDT
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