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

Fri Feb 6 15:48:44 CET 2015

I realized my mistake :) Sorry. There was a few missing atoms and residues
in the .pdb file. I had completed them using pymol and amber xleap tool. I
hadnt used chain identifier while i added these missing atoms to the .pdb
file. But the other all residues had a chain identifier in the .pdb file.
So pdb2gmx's head was confused. But it works now.

And as you said before
http://comments.gmane.org/gmane.science.biology.gromacs.user/62384 pdb2gmx
dont need to  the N and C prefixes in the 4.6.x series. I tested it.

2015-02-06 14:11 GMT+01:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> 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
>>>>>>>> --
>>>>>>>> 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
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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/
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-- 
Ahmet Yıldırım