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

[Ahmet yıldırım]

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?

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
>>>>>> --
>>>>>> Gromacs Users mailing list
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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
>>>
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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
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-- 
Ahmet Yıldırım