Re: [AMBER] Fwd: Re: files for RED

From: Urszula Uciechowska <urszula.uciechowska.chem.umu.se>
Date: Wed, 31 Oct 2012 08:55:35 +0100

Thank you Francois, is working now.

I have one more molecule, the charges were also calculated using RED server. I have just assigned the atom types however I am not quite sure if they are correct, could you please have a quick look?

Thank you in advance
Urszula


________________________________________
Von: FyD [fyd.q4md-forcefieldtools.org]
Gesendet: Dienstag, 30. Oktober 2012 11:54
An: AMBER Mailing List
Betreff: Re: [AMBER] Fwd: Re: files for RED

Urszula,

> Thank you for your files. I tried to use them and there is still an
> error. Below I pasted the steps that I did in xlep. What can be
> wrong there?
>
> MOL = loadmol2 MOL_param1.mol2
> Loading Mol2 file: ./MOL_param1.mol2
> Reading MOLECULE named MOL
>> set MOL name "MOL"
>> set MOL head MOL.1.N
>> set MOL tail MOL.1.C
>> set connect0 MOL.1.N
> set: Improper number of arguments!
> usage: set <container> <parameter> <object>
> or: set default <parameter> <value>
>> set MOL.1 connect0 MOL.1.N
>> set MOL.1 connect1 MOL.1.C
>> set MOL.1 restype protein
>> x = loadpdb protein.pdb
> Loading PDB file: ./protein.pdb
>
> check x
> Checking 'x'....
> WARNING: The unperturbed charge of the unit: -9.000000 is not zero.
> Warning: Close contact of 1.377996 angstroms between .R<GLN
> 176>.A<HE21 14> and .R<SER 208>.A<HG 9>
> Warning: Close contact of 1.118681 angstroms between .R<VAL 197>.A<H
> 2> and .R<HIE 223>.A<HD2 15>
> Warning: Close contact of 1.495391 angstroms between .R<THR
> 198>.A<HG1 12> and .R<ALA 477>.A<HA 4>
> Warning: Close contact of 1.101699 angstroms between .R<ARG
> 349>.A<HH22 22> and .R<THR 376>.A<HG1 12>
> Warning: Close contact of 0.926000 angstroms between .R<TYR
> 375>.A<HH 15> and .R<TRP 525>.A<HE1 12>
> Checking parameters for unit 'x'.
> Checking for bond parameters.
> Could not find bond parameter for: P - CT

-> you need to create a frcmod file; see for instance:
http://q4md-forcefieldtools.org/REDDB/projects/F-87/script3.ff

- the FF equilibrium value could come from a QM geometry optimization
performed using a large basis set + DFT
- the FF constant:
   - by analogy to an existing one, or
   - taken/adapted from gaff (capital letters + rounding off/average
the FF cst), or
   - from a QM fit

> Checking for angle parameters.
> Could not find angle parameter: CT - P - OS

-> yes this is normal; this one is not in parm99
same as above

> Could not find angle parameter: O2 - P - CT

-> yes this is normal; this one is not in parm99
same as above

> Could not find angle parameter: P - CT - HC

-> the FF cst should be 50

> Could not find angle parameter: HC - CT - OS

oh oh it looks like I did a mistake in my previous email;
it should be "H1 - CT - OS" which is known this one

regards, Francois


> .<TRIPOS>MOLECULE
> MOL
> 34 34 1 0 1
> SMALL
> USER_CHARGES
> .<TRIPOS>ATOM
> 1 N -3.388629 1.242931 -0.916676 N 1 MOL -0.4971
> 2 H -3.965446 1.340785 -1.720302 H 1 MOL 0.3334
> 3 CA -2.318783 0.258016 -1.020777 CT 1 MOL -0.0492
> 4 HA -2.170353 0.089287 -2.076625 H1 1 MOL 0.1199
> 5 CB -0.986035 0.784114 -0.469710 CT 1 MOL 0.0753
> 6 HB2 -0.833044 1.792017 -0.828299 H1 1 MOL 0.1137
> 7 HB3 -0.961267 0.781322 0.605434 H1 1 MOL 0.1137
> 8 OG 0.065502 -0.006616 -0.997491 OS 1 MOL -0.4784
> 9 P1 0.859423 -1.117194 -0.163621 P 1 MOL 1.0676
> 10 O1 0.267069 -1.361553 1.149275 O2 1 MOL -0.6687
> 11 C1 0.962427 -2.492936 -1.304974 CT 1 MOL -0.3402
> 12 H11 -0.035454 -2.860013 -1.505118 HC 1 MOL 0.1074
> 13 H12 1.558987 -3.281198 -0.861959 HC 1 MOL 0.1074
> 14 H13 1.424633 -2.176690 -2.232026 HC 1 MOL 0.1074
> 15 O2 2.358154 -0.607416 -0.122616 OS 1 MOL -0.4002
> 16 C20 2.917651 0.172050 0.949998 CT 1 MOL 0.1129
> 17 H20 2.325496 -0.009676 1.835773 H1 1 MOL 0.0643
> 18 C25 2.881146 1.652126 0.578287 CT 1 MOL -0.0505
> 19 H9 1.859352 1.952971 0.370806 HC 1 MOL 0.0299
> 20 H10 3.203877 2.219264 1.449359 HC 1 MOL 0.0299
> 21 C24 3.789162 1.973868 -0.611918 CT 1 MOL 0.0017
> 22 H5 3.393061 1.496379 -1.503272 HC 1 MOL 0.0059
> 23 H6 3.780198 3.044283 -0.797882 HC 1 MOL 0.0059
> 24 C23 5.222129 1.491734 -0.365834 CT 1 MOL 0.0076
> 25 H7 5.836808 1.687313 -1.240062 HC 1 MOL 0.0015
> 26 H14 5.657983 2.061053 0.454263 HC 1 MOL 0.0015
> 27 C22 5.256053 -0.000484 -0.021725 CT 1 MOL 0.0017
> 28 H15 4.936824 -0.578638 -0.883843 HC 1 MOL 0.0059
> 29 H16 6.272165 -0.310322 0.205854 HC 1 MOL 0.0059
> 30 C21 4.344134 -0.320012 1.166319 CT 1 MOL -0.0505
> 31 H17 4.728819 0.162271 2.062879 HC 1 MOL 0.0299
> 32 H18 4.325153 -1.387024 1.361876 HC 1 MOL 0.0299
> 33 C -2.670348 -1.126643 -0.454803 C 1 MOL 0.6178
> 34 O -2.493761 -2.101306 -1.141475 O 1 MOL -0.5632
> .<TRIPOS>BOND
> 1 1 2 1
> 2 1 3 1
> 3 3 4 1
> 4 3 5 1
> 5 3 33 1
> 6 5 6 1
> 7 5 7 1
> 8 5 8 1
> 9 8 9 1
> 10 9 10 1
> 11 9 11 1
> 12 9 15 1
> 13 11 12 1
> 14 11 13 1
> 15 11 14 1
> 16 15 16 1
> 17 16 17 1
> 18 16 18 1
> 19 16 30 1
> 20 18 19 1
> 21 18 20 1
> 22 18 21 1
> 23 21 22 1
> 24 21 23 1
> 25 21 24 1
> 26 24 25 1
> 27 24 26 1
> 28 24 27 1
> 29 27 28 1
> 30 27 29 1
> 31 27 30 1
> 32 30 31 1
> 33 30 32 1
> 34 33 34 1
> .<TRIPOS>SUBSTRUCTURE
> 1 MOL 1 **** 0 **** ****
>
>
> ----- Forwarded message from fyd.q4md-forcefieldtools.org -----
> Date: Sun, 28 Oct 2012 17:53:44 +0100
> From: FyD <fyd.q4md-forcefieldtools.org>
> Reply-To: FyD <fyd.q4md-forcefieldtools.org>
> Subject: Re: [AMBER] files for RED
> To: AMBER Mailing List <amber.ambermd.org>
>
> Dear Urszula,
>
>> I obtained the geometry from the RED server. Now I was wondering if
>> I should use the amber99 atom types like MOL_p1.mol2 or
>> apply gaff and use the MOL.mol2? Anyway in both cases I am getting
>> some errors about missing parameters.
>
> I would not use GAFF as this is a modified amino-acid.
> Below are the FF atom types, which are corrected...
>
> You could load leaprc.ff99SB and edit "DC" and "ALA" to get some ideas
> about these FF atom types...
>
>> Could you please suggest me how to correct them? and which option
>> should I use?
>
> you might have to compute some dihedral angles you judge important...
>
> regards, Francois
>
>
> .<TRIPOS>MOLECULE
> MOL
> 34 34 1 0 1
> SMALL
> USER_CHARGES
> .<TRIPOS>ATOM
> 1 N -3.388629 1.242931 -0.916676 N 1 MOL -0.4971
> 2 H -3.965446 1.340785 -1.720302 H 1 MOL 0.3334
> 3 CA -2.318783 0.258016 -1.020777 CT 1 MOL -0.0492
> 4 HA -2.170353 0.089287 -2.076625 H1 1 MOL 0.1199
> 5 CB -0.986035 0.784114 -0.469710 CT 1 MOL 0.0753
> 6 HB2 -0.833044 1.792017 -0.828299 H1 1 MOL 0.1137
> 7 HB3 -0.961267 0.781322 0.605434 H1 1 MOL 0.1137
> 8 OG 0.065502 -0.006616 -0.997491 OS 1 MOL -0.4784
> 9 P1 0.859423 -1.117194 -0.163621 P 1 MOL 1.0676
> 10 O1 0.267069 -1.361553 1.149275 O2 1 MOL -0.6687
> 11 C1 0.962427 -2.492936 -1.304974 CT 1 MOL -0.3402
> 12 H11 -0.035454 -2.860013 -1.505118 HC 1 MOL 0.1074
> 13 H12 1.558987 -3.281198 -0.861959 HC 1 MOL 0.1074
> 14 H13 1.424633 -2.176690 -2.232026 HC 1 MOL 0.1074
> 15 O2 2.358154 -0.607416 -0.122616 OS 1 MOL -0.4002
> 16 C20 2.917651 0.172050 0.949998 CG 1 MOL 0.1129
> 17 H20 2.325496 -0.009676 1.835773 H1 1 MOL 0.0643
> 18 C25 2.881146 1.652126 0.578287 CG 1 MOL -0.0505
> 19 H9 1.859352 1.952971 0.370806 HC 1 MOL 0.0299
> 20 H10 3.203877 2.219264 1.449359 HC 1 MOL 0.0299
> 21 C24 3.789162 1.973868 -0.611918 CG 1 MOL 0.0017
> 22 H5 3.393061 1.496379 -1.503272 HC 1 MOL 0.0059
> 23 H6 3.780198 3.044283 -0.797882 HC 1 MOL 0.0059
> 24 C23 5.222129 1.491734 -0.365834 CG 1 MOL 0.0076
> 25 H7 5.836808 1.687313 -1.240062 HC 1 MOL 0.0015
> 26 H14 5.657983 2.061053 0.454263 HC 1 MOL 0.0015
> 27 C22 5.256053 -0.000484 -0.021725 CG 1 MOL 0.0017
> 28 H15 4.936824 -0.578638 -0.883843 HC 1 MOL 0.0059
> 29 H16 6.272165 -0.310322 0.205854 HC 1 MOL 0.0059
> 30 C21 4.344134 -0.320012 1.166319 CG 1 MOL -0.0505
> 31 H17 4.728819 0.162271 2.062879 HC 1 MOL 0.0299
> 32 H18 4.325153 -1.387024 1.361876 HC 1 MOL 0.0299
> 33 C -2.670348 -1.126643 -0.454803 C 1 MOL 0.6178
> 34 O -2.493761 -2.101306 -1.141475 O 1 MOL -0.5632
> .<TRIPOS>BOND
> 1 1 2 1
> 2 1 3 1
> 3 3 4 1
> 4 3 5 1
> 5 3 33 1
> 6 5 6 1
> 7 5 7 1
> 8 5 8 1
> 9 8 9 1
> 10 9 10 1
> 11 9 11 1
> 12 9 15 1
> 13 11 12 1
> 14 11 13 1
> 15 11 14 1
> 16 15 16 1
> 17 16 17 1
> 18 16 18 1
> 19 16 30 1
> 20 18 19 1
> 21 18 20 1
> 22 18 21 1
> 23 21 22 1
> 24 21 23 1
> 25 21 24 1
> 26 24 25 1
> 27 24 26 1
> 28 24 27 1
> 29 27 28 1
> 30 27 29 1
> 31 27 30 1
> 32 30 31 1
> 33 30 32 1
> 34 33 34 1
> .<TRIPOS>SUBSTRUCTURE
> 1 MOL 1 **** 0 **** ****
>
>
>
>
>> Urszula,
>>
>>> The RED runs are finished, for the sarin the calculations are
>>> complete I guess, attached is obtained conformation
>>> Mol_m1-o1-sm_sarin.mol2?.
>>
>> Seems ok to me; see the attached image...
>>
>> And using LEaP I get:
>>
>> Welcome to LEaP!
>> (no leaprc in search path)
>>> X = loadmol2 Mol_m1-o1-sm_sarin.mol2
>> Loading Mol2 file: ./Mol_m1-o1-sm_sarin.mol2
>> Reading MOLECULE named MOL
>>> charge X
>> Total unperturbed charge: -0.000000
>> Total perturbed charge: -0.000000
>>
>>> However for the cyklosarin an error occurred, attached is log and
>>> p2n files for the cyklosarin.
>>> At the end of the cyklosarin file JOB1-gau_m1-1.com is:
>>> Sum of Mulliken charges with hydrogens summed into heavy atoms = 0.00000
>>> Error termination request processed by link 9999.
>>> Error termination via Lnk1e in /usr/local/g09-userred/l9999.exe at
>>> Wed Oct 24 19:34:57 2012.
>>> Job cpu time: 1 days 8 hours 5 minutes 14.2 seconds.
>>>
>>> Do you know, what did go wrong? how can I avoid this error?
>>
>> The R.E.D. log reports:
>>
>> Geometry optimization(s) is/are being computed for molecule 1 ...
>> [ FAILED ]
>> See the file(s) "JOB1-gau_m1-1.out"
>>
>> Geometry optimization convergence problem
>> Re-run the job using the best geometry obtained
>>
>> I think the structure did not converge in the Gaussian geometry
>> optimization; you have to select the best (or the last) "Standard
>> orientation" from the Gaussian log file; and copy the corresponding
>> Cartesian coordinates in the P2N file and re-run R.E.D.; the format of
>> the X, Y and Z columns in the P2N file does have to be strictly that
>> of the PDB file format; thus you can do a crude copy/cut of these
>> cart. coordinates taken from the Gaussian log into the P2N file...
>>
>> regards, Francois
>>
>>
>>> Dear Urszula,
>>>
>>>> I run RED 2.0 I hope that the p2n file are ok now. Could you please
>>>> have a look at them?
>>>> The additional H were removed, and the P atom is asymmetric that is
>>>> correct. The conformations of the
>>>> sarin and cyklosarin were taken from the xray structures.
>>>
>>> Chemical equivalencing is correct this time.
>>>
>>> You use a single INTRA-MCC for the 2 capping groups; strictly, this is
>>> correct, but this is not the 'Amber' approach, where an intra-mcc set
>>> to zero is used for each capping group.
>>>
>>> Do you agree with the conformation you generated? is it in agreement
>>> with experimental data? and/or is it the lowest minimum? an
>>> alternative could be to split this whole molecule into two building
>>> blocks.
>>>
>>> regards, Francois
>>>
>>>
>>>> Dear Urszula,
>>>>
>>>>> I prepared two p2n files for RED server ( sarin and cykosarin).
>>>>> However I am not quite sure if they are correct or I need to add
>>>>> something else.
>>>>
>>>> You used Ante_R.E.D. 1.x to generate these P2N files; please use
>>>> instead R.E.D. Server/Ante_R.E.D. 2.0 because Ante_R.E.D. 1.x does not
>>>> handle chemical equivalencing between different chemical groups;
>>>> See http://q4md-forcefieldtools.org/REDS/news.php
>>>> http://q4md-forcefieldtools.org/REDS/news.php#2
>>>> http://q4md-forcefieldtools.org/REDS/popup/popanteredtopequiv.php
>>>>
>>>> For Sarin, the two terminal methyl groups in the side chain should be
>>>> equivalenced; i.e. they should bear both the following names: CT16 H16
>>>> H16 H16 or both CT17 H17 H17 H17
>>>>
>>>> For cyclosarin, same type of remarks for the methylene group in the
>>>> pseudo cyclohexane group: CT15 and CT19 should bear the same number;
>>>> same remark for CT16 and CT18.
>>>> You have two additional hydrogen atoms in this dipeptide; I am not
>>>> sure this is correct...
>>>>
>>>> then, I would check that the optimized geometry for each of these
>>>> dipeptides corresponds to what I want after geometry optimization.
>>>>
>>>> finally, is your P atom asymmetric?
>>>>
>>>> regards, Francois
>
>
> ----- End forwarded message -----
>
>
>
>
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> AMBER.ambermd.org
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>



           F.-Y. Dupradeau
                 ---
http://q4md-forcefieldtools.org/FyD/


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Received on Wed Oct 31 2012 - 01:30:04 PDT
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