[gmx-users] Error: Atomtype CH2 not found

[Justin Lemkul]

On 12/14/19 1:14 PM, Paul Buscemi wrote:
> If the itp is correct then modify atomnames2types to add the correct bonds and bond lengths

The atomname2type.n2t file is only relevant with x2top, but the OP 
already has a topology, so this is not the issue. If you mean the .atp 
file, then this too is not relevant because pdb2gmx is the only program 
that reads this.

-Justin

> PB
>
>> On Dec 13, 2019, at 7:52 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>>> On 12/13/19 2:18 AM, Muthusankar wrote:
>>> Dear Gromacs users,
>>> I am simulating a protein-ligand complex and performing the grompp command
>>> before adding ions to the system. I got the error.
>>> *Fatal error: *(file: ligand.itp)
>>> Atomtype *CH2 not found*.
>>> *command used:*
>>> gmx grompp -f ions.mdp -c protein_box.gro -p protein.top -o ions.tpr
>>>
>>> Please guide me, How to rectify the problem.
>>>
>> This means you're trying to use an atom type that your force field doesn't recognize. Either you're mixing and matching force fields (never do this) or your ligand topology relies on new atom types that should be introduced into the force field, in which case the source of the ligand topology (server, etc.) should provide that information.
>>
>> -Justin
>>
>> -- 
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================