[gmx-users] topology

RAHUL SURESH drrahulsuresh at gmail.com
Thu Mar 2 14:38:05 CET 2017


Nope.. I havent tried that one.

If I am manually parametrizing a topology, then i shud add them in
aminoacids .rtp file? Should I make any change to gro file?

On Thu, Mar 2, 2017 at 6:56 PM, Jakub Krajniak <
jakub.krajniak at cs.kuleuven.be> wrote:

> Did you try mktop ? (http://www.aribeiro.net.br/mktop)
>
>
>
> On 02.03.2017 05:23, RAHUL SURESH wrote:
>
>> Dear Justin
>>
>> Is there anything I can do to make this job easier?
>>
>> On Thu, Mar 2, 2017 at 1:02 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>> On 3/1/17 2:19 PM, RAHUL SURESH wrote:
>>>
>>> Dear Justin
>>>>
>>>> What is the error here?
>>>> I don't understand it.
>>>> Can you be little more precise?
>>>>
>>>>
>>>> The long and short of it TopolGen is very crudely coded and atom order
>>> matters because the script makes a lot of assumptions.  Your input PDB
>>> file
>>> has atoms grouped by element (O,O,C,C,C,C,H...) so TopolGen can't figure
>>> out what any of the actual functional groups are, so you get basically
>>> default atom types for everything.
>>>
>>> -Justin
>>>
>>>
>>> On Wed, Mar 1, 2017 at 1:58 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>>
>>>> On 2/28/17 3:24 AM, RAHUL SURESH wrote:
>>>>>
>>>>> This is my itp file(only a part)
>>>>>
>>>>>> I have highlighted two errors.. there are 19 such errors.
>>>>>> If I can know the reason for the error exactly it would be of a great
>>>>>> help
>>>>>> to me.
>>>>>>
>>>>>>
>>>>>> TopolGen relies on atom ordering to guess what the proper parameters
>>>>>>
>>>>> should be. It's pretty limited in what it can do.  A coordinate file
>>>>> that
>>>>> simply groups atoms by element is going to produce a totally garbage
>>>>> topology, unfortunately.
>>>>>
>>>>> -Justin
>>>>>
>>>>>
>>>>> [ atoms ]
>>>>>
>>>>>> ;   nr       type  resnr residue  atom   cgnr     charge       mass
>>>>>> typeB    chargeB      massB
>>>>>>       1   opls_154      1    UNK      O      0     -0.580921
>>>>>> 15.99940
>>>>>>       2   opls_154      1    UNK      O      0     -0.635654
>>>>>> 15.99940
>>>>>>       3   opls_516      1    UNK      C      1     -0.112257
>>>>>> 12.01100
>>>>>>       4   opls_516      1    UNK      C      2     -0.163224
>>>>>> 12.01100
>>>>>>       5   opls_516      1    UNK      C      3      0.228741
>>>>>> 12.01100
>>>>>>       6   opls_516      1    UNK      C      4     -0.304756
>>>>>> 12.01100
>>>>>>       7   opls_516      1    UNK      C      5     -0.312217
>>>>>> 12.01100
>>>>>>       8   opls_145      1    UNK      C      6      0.120569
>>>>>> 12.01100
>>>>>>       9   opls_145      1    UNK      C      7      0.151897
>>>>>> 12.01100
>>>>>>      10   opls_145      1    UNK      C      8      0.231044
>>>>>> 12.01100
>>>>>>      11   opls_516      1    UNK      C      9     -0.401751
>>>>>> 12.01100
>>>>>>      12   opls_516      1    UNK      C     10     -0.403094
>>>>>> 12.01100
>>>>>>      13   opls_145      1    UNK      C     11     -0.150352
>>>>>> 12.01100
>>>>>>      14   opls_145      1    UNK      C     12      0.193129
>>>>>> 12.01100
>>>>>>      15   opls_145      1    UNK      C     13     -0.161115
>>>>>> 12.01100
>>>>>>      16   opls_516      1    UNK      C     14     -0.471874
>>>>>> 12.01100
>>>>>>      17   opls_145      1    UNK      C     15      0.100725
>>>>>> 12.01100
>>>>>>      18   opls_145      1    UNK      C     16     -0.153943
>>>>>> 12.01100
>>>>>>      19   opls_516      1    UNK      C     17     -0.330577
>>>>>> 12.01100
>>>>>>      20   opls_516      1    UNK      C     18     -0.229875
>>>>>> 12.01100
>>>>>>      21   opls_135      1    UNK      C     19     -0.229884
>>>>>> 12.01100
>>>>>>      22   opls_135      1    UNK      C     20     -0.237230
>>>>>> 12.01100
>>>>>>      23   opls_135      1    UNK      C     21     -0.404861
>>>>>> 12.01100
>>>>>>      24   opls_140      1    UNK      H     21      0.135257
>>>>>> 1.00800
>>>>>>      25   opls_140      1    UNK      H     21      0.154010
>>>>>> 1.00800
>>>>>>      26   opls_140      1    UNK     2H     21      0.142643
>>>>>> 1.00800
>>>>>>      27   opls_140      1    UNK     1H     21      0.133623
>>>>>> 1.00800
>>>>>>      28   opls_140      1    UNK     2H     21      0.137323
>>>>>> 1.00800
>>>>>>      29   opls_140      1    UNK     1H     21      0.167475
>>>>>> 1.00800
>>>>>>      30   opls_140      1    UNK     1H     21      0.135348
>>>>>> 1.00800
>>>>>>      31   opls_140      1    UNK     2H     21      0.153851
>>>>>> 1.00800
>>>>>>      32   opls_140      1    UNK     3H     21      0.138487
>>>>>> 1.00800
>>>>>>      33   opls_140      1    UNK     1H     21      0.137087
>>>>>> 1.00800
>>>>>>      34   opls_140      1    UNK     2H     21      0.146500
>>>>>> 1.00800
>>>>>>      35   opls_140      1    UNK     3H     21      0.148972
>>>>>> 1.00800
>>>>>>      36   opls_140      1    UNK      H     21      0.103605
>>>>>> 1.00800
>>>>>>      37   opls_140      1    UNK      H     21      0.127061
>>>>>> 1.00800
>>>>>>      38   opls_140      1    UNK     1H     21      0.143100
>>>>>> 1.00800
>>>>>>      39   opls_140      1    UNK     2H     21      0.137525
>>>>>> 1.00800
>>>>>>      40   opls_140      1    UNK     3H     21      0.140672
>>>>>> 1.00800
>>>>>>      41   opls_140      1    UNK      H     21      0.106416
>>>>>> 1.00800
>>>>>>      42   opls_140      1    UNK     1H     21      0.134610
>>>>>> 1.00800
>>>>>>      43   opls_140      1    UNK     2H     21      0.126890
>>>>>> 1.00800
>>>>>>      44   opls_140      1    UNK     2H     21      0.132690
>>>>>> 1.00800
>>>>>>      45   opls_140      1    UNK     1H     21      0.124796
>>>>>> 1.00800
>>>>>>      46   opls_140      1    UNK      H     21      0.371894
>>>>>> 1.00800
>>>>>>      47   opls_140      1    UNK     1H     21      0.120642
>>>>>> 1.00800
>>>>>>      48   opls_140      1    UNK     2H     21      0.117792
>>>>>> 1.00800
>>>>>>      49   opls_140      1    UNK     2H     21      0.125342
>>>>>> 1.00800
>>>>>>      50   opls_140      1    UNK     1H     21      0.122930
>>>>>> 1.00800
>>>>>>      51   opls_140      1    UNK     1H     21      0.130012
>>>>>> 1.00800
>>>>>>      52   opls_140      1    UNK     2H     21      0.129674
>>>>>> 1.00800
>>>>>>      53   opls_140      1    UNK     3H     21      0.131255
>>>>>> 1.00800
>>>>>>
>>>>>> [ bonds ]
>>>>>> ;  ai    aj funct
>>>>>>      1     5     1    ;     O     C
>>>>>>      1    10     1    ;     O     C
>>>>>>      2    14     1    ;     O     C
>>>>>>      *2    46     1    ;     O     H*
>>>>>>
>>>>>>      3     4     1    ;     C     C
>>>>>>      3     5     1    ;     C     C
>>>>>>      3     6     1    ;     C     C
>>>>>>      3    24     1    ;     C     H
>>>>>>      4     7     1    ;     C     C
>>>>>>      4     8     1    ;     C     C
>>>>>>      4    25     1    ;     C     H
>>>>>>      5    11     1    ;     C     C
>>>>>>      5    12     1    ;     C     C
>>>>>>      6    13     1    ;     C     C
>>>>>>      6    26     1    ;     C    2H
>>>>>>      6    27     1    ;     C    1H
>>>>>>      7     9     1    ;     C     C
>>>>>>      7    28     1    ;     C    2H
>>>>>>      7    29     1    ;     C    1H
>>>>>>      8    10     1    ;     C     C
>>>>>>      8    14     1    ;     C     C
>>>>>>      9    13     1    ;     C     C
>>>>>>      9    16     1    ;     C     C
>>>>>>     10    15     1    ;     C     C
>>>>>>     11    30     1    ;     C    1H
>>>>>>     11    31     1    ;     C    2H
>>>>>>     11    32     1    ;     C    3H
>>>>>>     12    33     1    ;     C    1H
>>>>>>     12    34     1    ;     C    2H
>>>>>>     12    35     1    ;     C    3H
>>>>>>     *13    36     1    ;     C     H*
>>>>>>
>>>>>>     14    18     1    ;     C     C
>>>>>>     15    17     1    ;     C     C
>>>>>>     15    37     1    ;     C     H
>>>>>>     16    38     1    ;     C    1H
>>>>>>     16    39     1    ;     C    2H
>>>>>>     16    40     1    ;     C    3H
>>>>>>     17    18     1    ;     C     C
>>>>>>     17    19     1    ;     C     C
>>>>>>     18    41     1    ;     C     H
>>>>>>     19    20     1    ;     C     C
>>>>>>     19    42     1    ;     C    1H
>>>>>>     19    43     1    ;     C    2H
>>>>>>     20    21     1    ;     C     C
>>>>>>     20    44     1    ;     C    2H
>>>>>>     20    45     1    ;     C    1H
>>>>>>     21    22     1    ;     C     C
>>>>>>     21    47     1    ;     C    1H
>>>>>>     21    48     1    ;     C    2H
>>>>>>     22    23     1    ;     C     C
>>>>>>     22    49     1    ;     C    2H
>>>>>>     22    50     1    ;     C    1H
>>>>>>     23    51     1    ;     C    1H
>>>>>>     23    52     1    ;     C    2H
>>>>>>     23    53     1    ;     C    3H
>>>>>>
>>>>>> On Tue, Feb 28, 2017 at 3:57 AM, Justin Lemkul <jalemkul at vt.edu>
>>>>>> wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>> On 2/27/17 12:49 AM, RAHUL SURESH wrote:
>>>>>>>
>>>>>>> I am explaining my issues regarding complex simulation.
>>>>>>>
>>>>>>> I have 200ns conformer(OPLS FF)
>>>>>>>>
>>>>>>>> I have generated my ligand gro and itp file.(Using topolgen1_1)
>>>>>>>>
>>>>>>>> I have edited my protein gro file and made it into complex file as
>>>>>>>> per
>>>>>>>> the
>>>>>>>> tutorials.
>>>>>>>>
>>>>>>>> I have made changes to my topol.top file.
>>>>>>>>
>>>>>>>> Now in my command for em.mdp I am getting 19 errors stating "NO
>>>>>>>> DEFAULT
>>>>>>>> BOND TYPE, ANGLE TYPE, ETC."
>>>>>>>>
>>>>>>>> Can you guide me with this?
>>>>>>>>
>>>>>>>>
>>>>>>>> This means the atom type assignment makes reference to bonded
>>>>>>>> parameters
>>>>>>>>
>>>>>>>> that don't exist.  That means one of two things: (1) either the atom
>>>>>>> type
>>>>>>> assignment is incorrect, requiring manual correction (as the script
>>>>>>> warns
>>>>>>> you, as it makes a lot of assumptions and is therefore rather dumb
>>>>>>> sometimes) or (2) you simply have a molecule for which parameters do
>>>>>>> not
>>>>>>> exist, requiring manual parametrization.  For OPLS-AA, this requires
>>>>>>> QM
>>>>>>> calculations to get things like equilibrium geometries, vibrational
>>>>>>> frequencies, and dihedral potential energy scans.
>>>>>>>
>>>>>>>
>>>>>>> -Justin
>>>>>>>
>>>>>>> --
>>>>>>> ==================================================
>>>>>>>
>>>>>>> Justin A. Lemkul, Ph.D.
>>>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>>>
>>>>>>> Department of Pharmaceutical Sciences
>>>>>>> School of Pharmacy
>>>>>>> Health Sciences Facility II, Room 629
>>>>>>> University of Maryland, Baltimore
>>>>>>> 20 Penn St.
>>>>>>> Baltimore, MD 21201
>>>>>>>
>>>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>>>
>>>>>>> ==================================================
>>>>>>> --
>>>>>>> Gromacs Users mailing list
>>>>>>>
>>>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>>>> /Mailing_Lists/GMX-Users_List before posting!
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>>>>>>>
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>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>>>>> or
>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> --
>>>>>>
>>>>> ==================================================
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>
>>>>> Department of Pharmaceutical Sciences
>>>>> School of Pharmacy
>>>>> Health Sciences Facility II, Room 629
>>>>> University of Maryland, Baltimore
>>>>> 20 Penn St.
>>>>> Baltimore, MD 21201
>>>>>
>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>> /Mailing_Lists/GMX-Users_List before posting!
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>>>>>
>>>>>
>>>>>
>>>>
>>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
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>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
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>>>
>>
>> --
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*


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