[gmx-users] Unknown bond_atomtype CAY
Sameer Edirisinghe
nootsam at gmail.com
Sun Sep 18 20:06:16 CEST 2016
Dear Dr. Justin,
If atom names names cant use in ffbonded.itp file how should i add bond
interaction used in .rtp file to ff..itp file ? this is the part i dont
understand. Do i need to modify ffnonbonded.itp file to correct the "Unknown
bond_atomtype' error which occurring while runing grompp ? If so how i
should modify ffnonbonded.itp (I have attached my .rtp file herewith)
Regards
Sameera
On Sun, Sep 18, 2016 at 10:45 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 9/18/16 1:12 PM, Sameer Edirisinghe wrote:
>
>> Dear Dr. Justin,
>>
>> Thanks for the reply. Following is the whole .rtp file i used. ( As you
>> said it was generated by using PRODRG)
>>
>>
> You shouldn't use the charges from PRODRG. They assume a united-atom
> force field, and are of very low quality. You can't force them into
> working with OPLS-AA. It's fundamentally wrong.
>
> If you want free help with a problem, you have to provide full
> information. Fragments of .rtp files are not helpful and it's a waste of
> time for those who are trying to give you advice.
>
>
> [ bondedtypes ]
>> ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih
>> 1 1 3 1
>>
>> ; MDI
>> [ MD ]
>> [ atoms ]
>> CAY opls_135 0 1
>> CAX opls_135 0.048 2
>> CAW opls_135 0.047 2
>> CAV opls_135 0.144 2
>> OAU opls_154 -0.112 2
>> CAS opls_131 0.219 2
>> OAT opls_236 -0.41 2
>> NAO opls_900 0.073 2
>> HAO opls_250 -0.009 2
>> CAE opls_260 0.056 3
>> CAF opls_145 -0.018 3
>> HAF opls_140 0.004 3
>> CAA opls_145 -0.018 3
>> HAA opls_140 0.004 3
>> CAD opls_145 -0.018 3
>> HAD opls_140 0.004 3
>> CAC opls_145 -0.018 3
>> HAC opls_140 0.004 3
>> CAB opls_145 -0.022 4
>> CAG opls_071 0.044 4
>> CAH opls_145 -0.022 4
>> CAM opls_145 -0.008 5
>> HAM opls_140 0.008 5
>> CAL opls_145 -0.008 6
>> HAL opls_140 0.008 6
>> CAI opls_145 -0.008 7
>> HAI opls_140 0.008 7
>> CAJ opls_145 -0.008 8
>> HAJ opls_140 0.008 8
>> CAK opls_145 0.072 9
>> NAN opls_900 0.072 9
>> HAN opls_250 -0.009 9
>> CAP opls_131 0.214 9
>> OAQ opls_236 -0.419 9
>> OAR opls_154 -0.115 9
>> CAZ opls_135 0.14 9
>> CBA opls_135 0.045 9
>> CBB opls_135 0.01 10
>> CBC opls_135 -0.01 10
>> HA1 opls_140 -0.013 1
>> HA2 opls_140 -0.013 1
>> HA3 opls_140 -0.014 1
>> HAZ opls_140 -0.013 1
>> HA0 opls_140 -0.013 1
>> HAX opls_140 -0.013 1
>> HAY opls_140 -0.013 1
>> HAV opls_140 -0.013 1
>> HAW opls_140 -0.013 1
>> HAG opls_140 -0.013 1
>> HAH opls_140 -0.013 1
>> HA4 opls_140 -0.013 1
>> HA5 opls_140 -0.013 1
>> HBA opls_140 -0.013 1
>> HBB opls_140 -0.013 1
>> HBC opls_140 -0.013 1
>> HBD opls_140 -0.013 1
>> HBF opls_140 -0.013 1
>> HBG opls_140 -0.013 1
>> HBE opls_140 -0.013 1
>> [ bonds ]
>> CAY HA1
>> CAY HA2
>> CAY HA3
>> CAX CAY
>> CAX HAZ
>> CAX HA0
>> CAX CAW
>> CAW HAX
>> CAW HAY
>> CAW CAV
>> CAV HAV
>> CAV HAW
>> CAV OAU
>> CAS OAU
>> CAS OAT
>> CAS NAO
>> NAO HAO
>> CAE NAO
>> CAE CAF
>> CAE CAD
>> CAF HAF
>> CAF CAA
>> CAA HAA
>> CAB CAA
>> CAD HAD
>> CAD CAC
>> CAC HAC
>> CAB CAC
>> CAB CAG
>> CAG HAG
>> CAG HAH
>> CAH CAG
>> CAH CAM
>> CAH CAI
>> CAM HAM
>> CAM CAL
>> CAL HAL
>> CAK CAL
>> CAI HAI
>> CAI CAJ
>> CAJ HAJ
>> CAK CAJ
>> CAK NAN
>> NAN HAN
>> CAP NAN
>> CAP OAQ
>> CAP OAR
>> CAZ OAR
>> CAZ HA4
>> CAZ HA5
>> CAZ CBA
>> CBA HBA
>> CBA HBB
>> CBA CBB
>> CBB HBC
>> CBB HBD
>> CBB CBC
>> CBC HBF
>> CBC HBG
>> CBC HBE
>>
>> ffbonded.itp file modified with the relevant bonds as below (part has
>> mentioned below)
>>
>> CAY HA1 1 0.10900 284512.0 ;
>> CAY HA2 1 0.10900 284512.0 ;
>> CAY HA3 1 0.10900 284512.0 ;
>> CAX CAY 1 0.15220 265265.6 ;
>> CAX HAZ 1 0.10900 284512.0 ;
>>
>>
>>
> As I said before, you cannot use atom names in ffbonded.itp.
>
> I know atom name is irrelevant but im bit confused how to write .rtp
>> without names for my 59 atom molecule.
>>
>>
> The .rtp file *does* use atom names. See the manual. That part is fine.
> What you cannot do is try to assign parameters using names. Those require
> types.
>
> -Justin
>
>
>
>> regards
>>
>> On Sun, Sep 18, 2016 at 10:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 9/18/16 12:30 PM, Sameer Edirisinghe wrote:
>>>
>>> Dear users,
>>>> There is one thing i cannot clarify from gromacs manual which is about
>>>> following error occurred while running grompp
>>>>
>>>> Fatal error:
>>>> Unknown bond_atomtype CAY
>>>>
>>>> I used to create .rtp file from atom types which are already defined in
>>>> atomtype.atp file. But still above error occurring while running
>>>> grompp.
>>>> Not sure should i add again thes atoms to atp file and if so how to add
>>>> them. Part of my rtp file is as below, I have modified the ffbonded.itp
>>>> (only bond types added) successfully.
>>>>
>>>>
>>>> What did you add to ffbonded.itp? Whatever it was is causing an error.
>>> Based on the .rtp entry below, it looks like you tried to use atom names
>>> in
>>> ffbonded.itp. That's not right. All interactions (bonded and nonbonded)
>>> are defined by atom type. The name is irrelevant. If you're re-using
>>> only
>>> OPLS-AA atom types, most of the bonded interactions should be present
>>> already.
>>>
>>> [ bondedtypes ]
>>>
>>>> ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14
>>>> RemoveDih
>>>> 1 1 3 1
>>>>
>>>>
>>>> You're missing entries here if you're trying to create an OPLS-derived
>>> force field. Look at oplsaa.ff/aminoacids.rtp
>>>
>>> ; MDI
>>>
>>>> [ MD ]
>>>> [ atoms ]
>>>> CAY opls_135 0.000 1
>>>> CAX opls_135 0.048 2
>>>> CAW opls_135 0.047 2
>>>> CAV opls_135 0.144 2
>>>> OAU opls_154 -0.112 2
>>>>
>>>>
>>>> This can't possibly be right. You've defined only heavy atoms (OPLS-AA
>>> is
>>> an all-atom force field, so there should be H) and the net charge of this
>>> residue is +0.117, which is physical nonsense. Based on the names and
>>> suspect charges, it looks like you're just porting over a PRODRG
>>> united-atom topology and trying to call it OPLS-AA. That's not going to
>>> work.
>>>
>>> Note that you also need [bonds] if you want the residue to actually be
>>> chemically reasonable, otherwise it's just a collection of atoms sitting
>>> near one another, which will immediately explode if you try to run a
>>> simulation.
>>>
>>> -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
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
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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
>
> ==================================================
> --
> Gromacs Users mailing list
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