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

[Justin Lemkul]

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
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Virginia Tech Department of Biochemistry
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