[gmx-users] topology
Jakub Krajniak
jakub.krajniak at cs.kuleuven.be
Thu Mar 2 14:36:01 CET 2017
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!
>>>>>>
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>
>>>>>> * For (un)subscribe requests visit
>>>>>> 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!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> 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!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
>
More information about the gromacs.org_gmx-users
mailing list