[gmx-users] Unknown bond_atomtype CAY
Sameer Edirisinghe
nootsam at gmail.com
Mon Sep 19 04:14:55 CEST 2016
Dear Dr. Justin,
If the bond types have not added, following errors occuring with grompp,
1) ERROR 1 [file topol.top, line 108]:
No default Bond types
2) ERROR 2 [file topol.top, line 168]:
No default Angle types
3) ERROR 3 [file topol.top, line 426]:
No default Ryckaert-Bell. types
Atom types are seems to be correct as i derived them from atomtype.atp
file.
If the interaction don't cover by the force field, how can I define them in
ffbonded.itp file ?
Regards
On Sep 19, 2016 3:57 AM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
> On 9/18/16 2:26 PM, Sameer Edirisinghe wrote:
>
>> 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 ?
>>
>>
> Determine if you need to in the first place. If grompp gives you errors
> about missing parameters, first verify that your choice of atom types is
> correct. Then, if there are in fact interactions that the force field
> doesn't cover:
>
> 1. Make sure your choice of force field was appropriate
> 2. Parametrize them in a manner consistent with the parent force field
>
> -Justin
>
> 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
>>>>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>>>>
>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>
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>>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>>>>> or
>>>>>>> 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
>>>>> /Mailing_Lists/GMX-Users_List before posting!
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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
>>> /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
>
> ==================================================
> --
> 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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