Dear George,
> This job, P5780, is now finished. Could you please post-process these data
> to generate the force field library, prep and frcmod files?
We will send to your personal email address four FF versions:
- AmberFF10 without lonepairs (for your modified dipeptide)
- AmberFF10 with lonepairs
- AmberFF99SB with lonepairs
- AmberFF99SB without lonepairs
this corresponds to four 'Re_fit' jobs performed with R.E.D. Python...
regards, Francois
>> 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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Received on Tue Jul 16 2013 - 08:30:02 PDT
