[gmx-users] no residue type with Amber99SB-ILDN ff

[Justin Lemkul]

On 2/6/15 8:10 AM, Ahmet yıldırım wrote:
> There isnt any breaks in chains. I checked it. But i use the middle domain
> of a structure. It means i deleted N-terminal and C-terminal domains. But
> it shouldnt be a problem?
>

Without seeing your full screen output and providing the PDB file for download 
somewhere, there's no point in guessing.  pdb2gmx finds a zwitterionic, 
standalone lysine.  Clearly there is a problem, otherwise pdb2gmx wouldn't tell 
you there is one :)

-Justin

> 2015-02-06 14:04 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>
>>
>>
>> On 2/6/15 8:03 AM, Ahmet yıldırım wrote:
>>
>>> LYS is NOT termini residue.
>>>
>>>
>> pdb2gmx thinks it is.  Check your input coordinate file (and screen
>> output, which tells you where any breaks in chains occur).
>>
>> -Justin
>>
>>
>>   2015-02-06 14:01 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:
>>>
>>>
>>>>
>>>> On 2/6/15 7:58 AM, Ahmet yıldırım wrote:
>>>>
>>>>   4 letter residue names of termini in pdb file are in the columns 18-22.
>>>>> I
>>>>> think they are correct columns?
>>>>>
>>>>>
>>>>>   The problem, from the error message, is that you have a standalone LYS
>>>> (a
>>>> zwitterion), so it is (in a sense) both NLYS and CLYS.  The Amber force
>>>> fields (as implemented) can't handle such a species due to modifications
>>>> of
>>>> backbone charges when applying N- and C-terminal modifications.  To use
>>>> this force field with this system, you need to introduce a new residue
>>>> that
>>>> defines the zwitterion correctly.
>>>>
>>>> -Justin
>>>>
>>>>
>>>>    2015-02-06 13:15 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:
>>>>
>>>>>
>>>>>    On Fri, Feb 6, 2015 at 12:43 PM, Ahmet yıldırım <ahmedo047 at gmail.com>
>>>>>
>>>>>> wrote:
>>>>>>
>>>>>>    Dear users,
>>>>>>
>>>>>>>
>>>>>>> I get the following error when i use pdb2gmx tool of GROMACS 4.6.5,
>>>>>>> with
>>>>>>> the AMBER99SB-ILDN ff. My command:
>>>>>>> pdb2gmx -f protein.pdb -o protein.gro -p protein.top
>>>>>>>
>>>>>>> Fatal error:
>>>>>>> In the chosen force field there is no residue type for 'LYS' as a
>>>>>>> standalone (starting & ending) residue
>>>>>>>
>>>>>>> The pdb2gmx gives this error though terminal residues are prefixed
>>>>>>> with
>>>>>>> N
>>>>>>> and C.
>>>>>>>
>>>>>>>
>>>>>>>   Maybe those prefixes are in the wrong columns of your input .pdb
>>>>>> file.
>>>>>>
>>>>>>
>>>>>>    Could there be something wrong with the input .pdb file? But i dont
>>>>>> get
>>>>>>
>>>>>>> this error with another forcefield, 43a2.
>>>>>>>
>>>>>>>
>>>>>>>   GROMOS force fields handle termini differently from AMBER, so that's
>>>>>> expected.
>>>>>>
>>>>>> Mark
>>>>>>
>>>>>>
>>>>>>
>>>>>>   --
>>>>>>> Ahmet Yıldırım
>>>>>>> --
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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
>>>>
>>>> ==================================================
>>>>
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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
>>
>> ==================================================
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>> 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

==================================================