Dear Francois
Thanks for these comments.
1) I looked at the conformation generated by the QM program. It is almost
identical with the input conformation (taken from a crystal structure)
and therefore looks very reasonable to me.
2) Concerning the molecular orientation procedure I am really unsure about
its effect on the calculation. I haven't touched any of the Mol_red*.p2n
files that were all generated automatically generated by the server.
Do you think I should include the same REMARK REORIENT statement:
REMARK REORIENT 1 5 7 | 7 5 1,
in all Mol_red*.p2n files for consistency? So to have the same orientation
procedure applied in all molecules?
If yes, I can edit the Mol_red*.p2n files accordingly but then I don't
know how to resubmit the job to the R.E.D server. Can you tell me how to
do this?
Best
George
> 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.:
> http://onlinelibrary.wiley.com/doi/10.1002/jcc.540161106/abstract 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
> optimization:
>
> 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
>
> egrep "REORIENT|TRANSLATE|ROTATE" P5749/*.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:
>>> 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
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Dr. George Patargias
Postdoctoral Researcher
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece
Office: +302106597568
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 10 2013 - 09:30:03 PDT
