Hello Francois
I had made the P2N file using the Ante_RED-1.5.pl script, from
RED-III.52-Tools-Files, that didn't insert the 'REMARK REORIENT' line.
I submitted to the server the P2N file that you generated
http://q4mdfft:q4mdfft2012.cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFjNd0qckaADFAZdGxKM9aL0w0g8OwT8SvADF/P5775.html
This job, P5780, is now finished. Could you please post-process these data
to generate the force field library, prep and frcmod files?
Thanks again.
George
> Dear George,
>
>> 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.
>
> This is just perfect... One should particularly check the optimized
> geometry if the molecule has a non-null total charge (your case).
>
>> 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.
>
> See the P2N file I generated using the non-automatic mode (to keep the
> 3 residues you defined) of R.E.D. Server/Ante_R.E.D. 2.0:
> http://q4mdfft:q4mdfft2012.cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFjNd0qckaADFAZdGxKM9aL0w0g8OwT8SvADF/P5775.html
> as you can see there is a 'REORIENT' line...
>
>> Do you think I should include the same REMARK REORIENT statement:
>> REMARK REORIENT 1 5 7 | 7 5 1,
>
> ok - why not - or simply use what Ante_R.E.D. 2.0 has generated...
>
>> in all Mol_red*.p2n files for consistency? So to have the same
>> orientation
>> procedure applied in all molecules?
>
> the idea is that the charge values become reproducible if the QMRA
> procedure is applied for all the molecules involved in charge
> derivation...
>
>> 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?
>
> Just resubmit your P2N file as you did it the first time:
> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
>
> if you want to save some cpu time, you could skip the geometry
> optimization step and provide the geometry optimization output
> generated by Gaussian with the P2N file and choose the mode 2 of
> R.E.D. Server/R.E.D. IV:
> See http://q4md-forcefieldtools.org/REDS/popup/popredmodes.php
>
> regards, Francois
>
>
>>> 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
>
>
>
>
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>
Dr. George Patargias
Postdoctoral Researcher
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece
Office: +302106597568
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Received on Thu Jul 11 2013 - 04:00:03 PDT
