[gmx-users] Error: Atomtype CH2 not found

[Justin Lemkul]

On 12/15/19 3:52 PM, paul buscemi wrote:
> Thank you for the clarification.  There’s a good chance there is more to this scenario   but I recall making polymers ( with Avogagdo ) , using pdb2gmx to create the top ( then itp )  and sometimes having the same error as the OP mentioned. The errors were eliminated by adding the unfound type with atomname2type.n2t
>
> I should be able to post the sequence of events if you think it useful to others.

If you have a useful and clear protocol for interoperability with other 
programs, sure, please post. But note that atomname2type.n2t files have 
nothing to do with pdb2gmx, and its contents certainly don't matter 
after a topology has been generated, so I'm not sure what you've been 
proposing.

-Justin

> Paul
>> On Dec 15, 2019, at 11:39 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>> 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
>>
>> ==================================================
>>
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>> Gromacs Users mailing list
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>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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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

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