[gmx-users] Residue not found in topology
jalemkul at vt.edu
Wed Aug 22 13:31:24 CEST 2018
On 8/22/18 5:26 AM, Bratin Kumar Das wrote:
> 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:
> On Wed 22 Aug, 2018, 2:53 PM Bratin Kumar Das, <177cy500.bratin at nitk.edu.in>
>> 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:
>>> line: 645
>>> Fatal error:
>>> Residue 'KAC' not found in residue topology database
>>> For more information and tips for troubleshooting, please check the
>>> 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!
>>> Gromacs Users mailing list
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> * 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.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
More information about the gromacs.org_gmx-users