[gmx-users] Residue 'UNK' not found in residue topology database

[Bratin Kumar Das]

You need to follow the procedure given in protein ligand system...Somehow
gromacs can't find the .itp file of the ligand which you added in your
topology file.

On Sat 7 Sep, 2019, 6:24 PM Navneet Kumar Singh, <navneetcdl at gmail.com>
wrote:

> Hello Everyone!
>
>
> I am trying to simulate 5 peptides, 10 small molecules (UNK) and water.
> I have used PACKMOL to make system having all these 3 ingredients.
> Peptides terminal residues were capped using ACE and NME in the pymol.
> It is pretty much straight forward simulating peptides with water as all
> necessary parameters are already defined.
> But When I am having UNK (A SMALL MOLECULE) in my system, its throwing
> error i.e. (Residue 'UNK' not found in residue topology database) and this
> is pretty much obvious that pdb2gmx can't find any UNK.
>
> During protein-ligand simulations we first get the .gro files for protein
> using pdb2gmx, similarly we prepare topology files for small molecules
> according to force field on some server or acpype. and then we combine the
> .gro files of protein and ligand, simultaneously update the topology files.
> then process continuous as usual.
>
> Here I have a .pdb file containing peptides and small molecules along with
> water prepared using the PACKMOL.
> How to deal with ligand. I have processed the one ligand according CHARMM
> force field (using CHARMM36 ) from CGenFF <https://cgenff.umaryland.edu/>.
> I have all .itp, .prm and other files. But how to add and proceed furthur?
>
>
>
>
>      Thanks & Regards
> _______________________________________________________
>
> [image: photo]
> *NAVNEET KUMAR*
>
> Doctoral Student
> Dept. of Pharmacoinformatics
> National Institute of Pharmaceutical Education and Research, Sector 67,
> S.A.S. Nagar - 160062, Punjab (INDIA)
>
> E navneetcdl at gmail.com  <navneetcdl at gmail.com>
>
> <http://www.linkedin.com/in/navneet-kumar-74391814a/>
> <http://facebook.com/xeon.singh> <http://instagram.com/snavneetkumar>
>
> Please consider your environmental responsibility. Before printing this
> e-mail message, ask yourself whether you really need a hard copy.
> --
> 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.
>