[gmx-users] grompp: unknown bond_atomtype

[Justin Lemkul]

On 4/1/15 4:27 PM, Alex wrote:
> I think I solved it already, thanks. Entirely due to horrible mess created
> by the necessity to create custom atom types. I wish you guys could make
> the bond length tolerance an input to x2top, I really do. :)
>

Well, I already showed you the function to modify to change it to your heart's 
desire ;)

-Justin

> On Wed, Apr 1, 2015 at 2:18 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 4/1/15 2:03 PM, Alex wrote:
>>
>>> I am working with a local copy of oplsaa.ff where I have defined a set of
>>> custom atom types in atomname2type.n2t and added the bond and angle
>>> parameters into ffbonded. x2top creates the topology without issues, but
>>> grompp reports a fatal error (see subject).
>>> The particular type it complains about is actually opls_335. Gromacs v.
>>> 4.6-beta3. Any ideas?
>>>
>>>
>> Don't use beta versions, especially ancient ones.
>>
>> The problem is related to a translated type; note that in ffnonbonded.itp
>> the second column is an atom type that is used in ffbonded.itp.  These are
>> different from the nonbonded types, but since there are fewer bonded types
>> to cover the parameters, these are used to remove redundancy.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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