[gmx-users] Residue BGC not found in the database

[Justin Lemkul]

On 2/27/19 10:17 AM, mary ko wrote:
>   Thanks Justin. How should I check if there is a Ter between protein and glucose ? If I get you right, for my protein and Bglc system I just need the Bgc in the .pdb to be changed to Bglc. Do I need to seprate Bglc from the protein and follow the tutorial or can it be regarded as a complex of protein-ligand and I can go ahead with pdb2gmx -f .pdb ?  I tried pdb2gmx and got this error  :  there were 233 missing atoms in molecule other, if you

If all residues are in the .rtp file, then pdb2gmx can generate the 
topology; this is a different case from when a ligand is unknown to the 
force field and must be dealt with separately.

233 missing atoms sounds like a lot - you must have something more than 
just a single glucose molecule. pdb2gmx won't be able to build missing H 
atoms without an .hdb entry, and that's probably what is going on here.

> want to use this incomplete topology anyhow use the option -missing. I continued with the-missing flag but there built an incomplete topology. In the energy minimizationit stops with the  :  'simulation ended prematurely no perrformance report will be written'. Should I continue regardless of the incomplete topology and this message ?

*Never* use pdb2gmx -missing to just bypass an error (there is only one 
case I have ever found -missing useful and it is mostly irrelevant 
nowadays). The resulting topology from pdb2gmx -missing is completely 
nonsensical.

-Justin

>      On Monday, February 25, 2019, 7:10:35 PM EST, Justin Lemkul <jalemkul at vt.edu> wrote:
>   
>   
>
> On 2/25/19 4:26 PM, mary ko wrote:
>>    Thank you Justin. I am actually following the protein-ligand tutorial to do simulations of my protein-ligand system. I skipped the python cgenff_charmm2gmx.py... Because of the mismatch of cgenff error couldnt be fixed. I have the bgc which is beta-D-glucose and built its .gro file as a ligand and protein-processed.gro and I copied the ligand in the protein-processed.gro to have the complex.gro. I also use charmm36-nov2018 and added it in the force fields with the Bglc to Bgc change in merged.rtp. Now that I try to build the topology.top file with pdb2gmx or even x2top there is an error: atom ot1 in residue Phe was not found in rtp entry Phe with 20 atoms while sorting atoms for pdb2gmx and could only find a force field type for 19078 out of 21750 atoms for x2top. What do you think I should do to build the topology?Thanks.
> If you have a protein with BGLC as the ligand, use pdb2gmx and make sure
> there is a TER between the protein and glucose, or otherwise a change in
> chain identifier. Do not use x2top and do not modify merged.rtp (modify
> the residue names in the PDB file instead).
>
> -Justin
>
>>        On Saturday, February 23, 2019, 6:50:39 PM EST, Justin Lemkul <jalemkul at vt.edu> wrote:
>>    
>>    
>>
>> On 2/20/19 11:19 AM, mary ko wrote:
>>> Dear all,
>>> I face the 'Residue BGC not found in the database' error when I try to build the topology file of my protein-ligand system by pdb2gmx -f pro.pdb. I used Charmm force field but I tried it with all the other force fields as well to see if the problem could be solved which was useless. I searched the list and errors-gromacs in the website and found that the simplest way is to change the name of this residue. As I am not familiar with protein structure, I do not know what changes may be helpful to pass this error. also, it is said that one way is to parameterize the residue which I do not know how to do that. Your help would be highly appreciated.Thanks!
>> If "BGC" is a synonym for beta-D-glucose, that is called BGLC in CHARMM,
>> so you just need to rename the residue accordingly. If it is some other
>> unknown species, then yes, you need to parametrize it yourself.
>>
>> -Justin
>>

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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