Dear Urszula,
> 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?
I would modify:
12 C2 -3.158820 2.095396 -1.063639 CT 1 MOL -0.0949
13 H21 -2.921131 2.565470 -0.122487 HC -> H1 1 MOL 0.0647
14 H22 -4.202083 2.282263 -1.292136 HC -> H1 1 MOL 0.0647
15 H23 -2.550371 2.540804 -1.847596 HC -> H1 1 MOL 0.0647
16 C1 -3.297453 -0.086298 -2.168517 CT 1 MOL -0.0949
17 H11 -3.181057 -1.147183 -2.001714 HC -> H1 1 MOL 0.0647
18 H12 -2.679839 0.203252 -3.014665 HC -> H1 1 MOL 0.0647
19 H13 -4.335473 0.106528 -2.414675 HC -> H1 1 MOL 0.0647
See $AMBERHOME/dat/leap/parm/parm99.dat
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
[...]
HC 1.008 0.135 H aliph. bond. to C without electrwd.group
H1 1.008 0.135 H aliph. bond. to C with 1 electrwd. group
N is a electrwd. group...
regards, Francois
> 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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Received on Wed Oct 31 2012 - 04:00:03 PDT
