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

Navneet Kumar Singh navneetcdl at gmail.com
Sat Sep 7 16:28:32 CEST 2019


I have 10 same ligands with different coordinates, as the ligands are
randomly distributed around the box. Do I have to do it manually. Even the
CGenFF will create the required .str files individually. How to deal with
this. I have seen in research articles people are using different small
molecules in different concentrations and simulate the whole system. I
think it would good to introduce and define separate topology parameter for
UNK. THen it will become a separate residue HETATM defined and pdb2gmx can
automatically use this.

On Sat, Sep 7, 2019 at 7:34 PM Bratin Kumar Das <177cy500.bratin at nitk.edu.in>
wrote:

> 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.
> >
> --
> 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.
>


-- 






     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)
P +918017967647  <+918017967647> |
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.


More information about the gromacs.org_gmx-users mailing list