[gmx-users] topology
Justin Lemkul
jalemkul at vt.edu
Thu Mar 2 13:48:57 CET 2017
On 3/1/17 11:23 PM, RAHUL SURESH wrote:
> Dear Justin
>
> Is there anything I can do to make this job easier?
>
Generate the small molecule coordinates based on a better program that does not
produce a difficult-to-use coordinate file, or choose a different force field
that has parametrization tools that make your life easier.
-Justin
> 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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>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>> ==================================================
>>>>
>>>> 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
>>
>> * 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
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>> 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
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