[gmx-users] Unknown bond_atomtype CAY

Sameer Edirisinghe nootsam at gmail.com
Sun Sep 18 20:26:58 CEST 2016


Dear Dr. Justin,

Now i can understand what what i have mistaken there. How can i derive
 [bondtypes]
for bonds i have used in .rtp file ?

Regards

On Sun, Sep 18, 2016 at 11:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>>>>>
>>>>> * Please search the archive at http://www.gromacs.org/Support
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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
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
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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
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>
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>
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