[gmx-users] Residue 'UNK' not found in residue topology database
Navneet Kumar Singh
navneetcdl at gmail.com
Sat Sep 7 19:13:45 CEST 2019
Thank You Sir!
I just removed the ligand part from the system.
Used Peptides+Water--Used pdb2gmx to create .gro file
converted the ligand.pdb in to .gro using command *gmx editconf -f unk.pdb
-o unk.gro*
combined the peptides+water.gro and ligand.gro to form ----complex.gro
updated the number of atoms.
Took a single UNK_fix.mol2 file and converted it to unk.itp file using the
method described in the protein-ligand complex tutorial at mdtutorials.com
Then updated the unk.itp and unk.prm file information in topol.top file.
Performed the energy minimization and everything went fine.
Sir is this right approach ?
On Sat, Sep 7, 2019 at 9:00 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 9/7/19 10:28 AM, Navneet Kumar Singh wrote:
> > How to do this. I am using CHARMM36 force-field.
> >
> > Even if I follow " adding a new residue to force field" from GROMACS
> > documentation. I have to add/modify several things. Like .rtp files;.hdb
> > files; atomtypes.atp etc. But to add these new parameters in these files
> ?
>
> If you already have an .itp file for the ligand, it is as simple as
> removing the coordinates from the starting structure, generating the
> protein topology with pdb2gmx, adding an #include statement for the
> ligand .itp file, and specifying 10 of the ligand in [molecules].
>
> -Justin
>
> > On Sat, Sep 7, 2019 at 7:54 PM Navneet Kumar Singh <navneetcdl at gmail.com
> >
> > wrote:
> >
> >> 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.
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> >>
> >> --
> >>
> >>
> >>
> >>
> >>
> >>
> >> 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.
> >>
> >>
> >>
> >>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
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>
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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
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