[gmx-users] topology

Subashini .K subashinik at hotmail.com
Thu Mar 2 08:51:57 CET 2017


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________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of RAHUL SURESH <drrahulsuresh at gmail.com>
Sent: Thursday, March 2, 2017 9:53 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] topology

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
[http://mackerell.umaryland.edu/~jalemkul/Images/lemkul_small.jpg]<http://mackerell.umaryland.edu/~jalemkul>

Justin A. Lemkul - MacKerell Lab<http://mackerell.umaryland.edu/~jalemkul>
mackerell.umaryland.edu
Welcome to my site! To learn more about me and the work I am doing, please use the navigation links above.


>>>>>
>>>>> ==================================================
>>>>> --
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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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>>>
>>
>>
>>
> --
> ==================================================
>
> 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
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--
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*
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