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

From: Urszula Uciechowska <urszula.uciechowska.chem.umu.se>
Date: Tue, 30 Oct 2012 09:54:51 +0100

Dear Francois,

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
Checking for angle parameters.
Could not find angle parameter: CT - P - OS
Could not find angle parameter: O2 - P - CT
Could not find angle parameter: P - CT - HC
Could not find angle parameter: P - CT - HC
Could not find angle parameter: P - CT - HC
Could not find angle parameter: OS - P - CT
Could not find angle parameter: HC - CT - OS
Could not find angle parameter: HC - CT - OS
There are missing parameters.
check: Warnings: 6
Unit is OK.
> quit

Thank you in advance for your suggestions

Urszula







Urszula Uciechowska, Ph.D.
Department of Chemistry
Umeň University
SE-901 87 Umeň, Sweden
urszula.uciechowska.chem.umu.se
________________________________________
Von: FyD [fyd.q4md-forcefieldtools.org]
Gesendet: Sonntag, 28. Oktober 2012 17:58
An: AMBER Mailing List
Betreff: [AMBER] Fwd: Re: files for RED

Urszula,

or you could even use: see below the new proposition;
this is not anymore a monosaccharide...

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 Tue Oct 30 2012 - 02:00:06 PDT
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