[gmx-users] grompp: unknown bond_atomtype

[Alex]

True, true. :)

On Wed, Apr 1, 2015 at 2:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
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> Gromacs Users mailing list
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