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

[Ahmet yıldırım]

LYS is NOT termini residue.

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
>>>>
>>>> * 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.
>>>>
>>>>  --
>>> 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.
>



-- 
Ahmet Yıldırım