[gmx-users] Unknown bond_atomtype CAY
Justin Lemkul
jalemkul at vt.edu
Sun Sep 18 20:09:09 CEST 2016
On 9/18/16 2:06 PM, Sameer Edirisinghe wrote:
> 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)
>
You do not need to modify ffnonbonded.itp.
You added an atom name in ffbonded.itp - this makes no sense and you cannot do
it. Bonded and nonbonded interactions are defined by type.
You must use atom names only in .rtp files, because the .rtp entry tells pdb2gmx
which atoms are bonded, and how. You can't do that by type because that is not
a unique way to identify connectivity. The list of [bonds] in the .rtp just
tells pdb2gmx which atoms are connect, it is separate from a [bondtypes]
directive, which says what parameters are assigned to each interaction type.
-Justin
>
> 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
>>
>> * Please search the archive at http://www.gromacs.org/Support
>> /Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>> send a mail to gmx-users-request at gromacs.org.
>>
>>
>>
--
==================================================
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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