Re: [AMBER] Methylated histidine lib and frcomd files

From: FyD <>
Date: Tue, 09 Jul 2013 15:09:16 +0200

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 || || || || || |
    -> Cu+ 28 (10) [Ar].3d10 || || || || ||
                                   -> 0 single electron
                                   -> spin multiplicity = 1
     -> 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 - 06:30:03 PDT
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