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

[Navneet Kumar Singh]

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 ?

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>
>> >
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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.
>
>
>
>

-- 






     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.