Re: [AMBER] Methylated histidine lib and frcomd files

From: FyD <>
Date: Wed, 10 Jul 2013 16:53:34 +0200

Dear George,

> The RED job P5749 with the methyl-histidine dipeptide has finished.

I looked at your P5749 data:

1) about the conformation of the dipeptide that R.E.D.
Server/Gaussian09 has generated:

See for instance: P5749/Data-R.E.D.Server/Mol_m1/Mol_m1-o1-qmra.pdb

Do you 'like' this conformation? i.e. is this conformation in
agreement with that _you want_ to get involved in charge derivation?
as the conformation strongly affect charge values many papers suggest
that one should always have a look at the optimized geometry generated
by a QM program. In short - one selects a conformation for charge
derivation that is close to that/these observed experimentally or See
Cieplak et al.: for
more information.

re-run R.E.D. Server until you 'like' the optimized geometry generated
for your dipeptide by changing the input geometry or by forcing the
use of dihedral (in your case) constraint(s) during geometry
optimization; in particular have a look at the phi, psi and chi1
dihedral angles...

2) about the molecular orientation procedure applied after geometry

ls -lv P5749/*.p2n
-rw-r--r-- 1 user user 3797 juil. 9 16:26 Mol_red1.p2n
-rw-r--r-- 1 user user 1261 juil. 9 16:26 Mol_red2.p2n
-rw-r--r-- 1 user user 3617 juil. 9 16:26 Mol_red3.p2n
-rw-r--r-- 1 user user 1097 juil. 9 16:26 Mol_red4.p2n
-rw-r--r-- 1 user user 3611 juil. 9 16:26 Mol_red5.p2n
-rw-r--r-- 1 user user 3501 juil. 9 16:26 Mol_red6.p2n

P5749/Mol_red2.p2n:REMARK REORIENT 1 5 7 | 7 5 1
P5749/Mol_red4.p2n:REMARK REORIENT 1 5 7 | 7 5 1

as you can see only the data that is stored internally (P2N files 2 &
4) by R.E.D. Server follow the 'RBRA' procedure, while your dipeptide
(molecules 1, 3, 5 and 6) does follow the 'QMRA' one; in other words
the re-orientation procedure (RBRA) of each optimized geometry is not
performed for the dipeptide you generated with Ante_R.E.D. 2.0; My
feeling is that Ante_R.E.D. 2.0 should have generated a keyword such
as 'REMARK REORIENT blabla (numbers)' in the p2N file; but it looks
like you remove this keyword. Could re-run the R.E.D. Server job
keeping this 'REMARK REORIENT blabla (numbers)' keyword.

Let me know what you decided...

> Would it be possible to post-process the R.E.D. Server/R.E.D. IV data to
> generate atom types, residue connections and frcmod files?

ok - no problem.

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 Wed Jul 10 2013 - 08:00:02 PDT
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