[gmx-users] no residue type with Amber99SB-ILDN ff
jalemkul at vt.edu
Fri Feb 6 14:01:22 CET 2015
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
> 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>
>>> 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
>>> 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
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Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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