[gmx-users] Residue not found in topology

[Justin Lemkul]

On 8/22/18 5:26 AM, Bratin Kumar Das wrote:
> Hi
>      In your tool.top file the particular lys molecule residue name you have
> to modify. Then it will work..Actually grompp can't find the molecule in
> the topology.

The error has nothing to do with grompp. The topology was never created 
because pdb2gmx could not write a topology for KAC.

CHARMM36 does support KAC, but not as a standalone residue. In CHARMM, 
one would generate a normal lysine then patch it with the KAC patch. To 
make this work in GROMACS, one would have to create a KAC .rtp entry by 
applying the same logic - modify LYS according to the KAC patch (found 
in the stream/prot/toppar_all36_prot_modify_res.str file from the 
tarball distributed by Alex MacKerell: 
http://mackerell.umaryland.edu/charmm_ff.shtml#charmm).

-Justin

> On Wed 22 Aug, 2018, 2:53 PM Bratin Kumar Das, <177cy500.bratin at nitk.edu.in>
> wrote:
>
>> Hi
>>      In your tool.top file the particular lys molecule residue name you
>> have to modify. Then it will work..Actually grompp can't find the molecule
>> in the topology.
>>
>> On Wed 22 Aug, 2018, 11:35 AM Amir Zeb, <zebamir85 at gmail.com> wrote:
>>
>>> Hi gromacs users,
>>>
>>> I want to simulate a protein where one of the lysine residues is modified
>>> to acetylated lysine and has been denoted by KAC. I want to simulate it by
>>> CharmM 36 ff, but it gave me this error.
>>>
>>>
>>> Program gmx pdb2gmx, VERSION 5.1.4
>>> Source code file:
>>> /home/chip/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/resall.c,
>>> line: 645
>>>
>>> Fatal error:
>>> Residue 'KAC' not found in residue topology database
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>>
>>>
>>> Is CharmM 36 ff capable to simulate modified residue acetylated lysine?
>>> If yes, what is the ff compatible notation for acetylated lysine?
>>> If not, which ff can I use to simulate acetylated lysine?
>>>
>>> Thanks in advance!
>>>
>>> Amir
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
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