[gmx-users] Re: How to add dihedral information from the GAFF topology
Justin A. Lemkul
jalemkul at vt.edu
Wed Mar 28 01:20:46 CEST 2012
bipin singh wrote:
> Thanks for your suggestions.
>
> Now I am getting the following error during grompp
>
> Warning: atom name 1 in topol.top and box_prot_oct_sol.gro does not
> match (C1 - N)
> Warning: atom name 5 in topol.top and box_prot_oct_sol.gro does not
> match (C2 - CA)
> Warning: atom name 6 in topol.top and box_prot_oct_sol.gro does not
> match (H4 - HA)
> Warning: atom name 7 in topol.top and box_prot_oct_sol.gro does not
> match (H5 - CB)
> Warning: atom name 8 in topol.top and box_prot_oct_sol.gro does not
> match (C3 - HB1)
> Warning: atom name 9 in topol.top and box_prot_oct_sol.gro does not
> match (H6 - HB2)
> Warning: atom name 10 in topol.top and box_prot_oct_sol.gro does not
> match (H7 - OG)
> Warning: atom name 11 in topol.top and box_prot_oct_sol.gro does not
> match (C4 - HG)
> Warning: atom name 12 in topol.top and box_prot_oct_sol.gro does not
> match (H8 - C)
> Warning: atom name 13 in topol.top and box_prot_oct_sol.gro does not
> match (H9 - O)
> Warning: atom name 14 in topol.top and box_prot_oct_sol.gro does not
> match (C5 - N)
> Warning: atom name 15 in topol.top and box_prot_oct_sol.gro does not
> match (H10 - H)
> Warning: atom name 16 in topol.top and box_prot_oct_sol.gro does not
> match (H11 - CA)
> Warning: atom name 17 in topol.top and box_prot_oct_sol.gro does not
> match (C6 - HA)
> Warning: atom name 18 in topol.top and box_prot_oct_sol.gro does not
> match (H12 - CB)
> Warning: atom name 19 in topol.top and box_prot_oct_sol.gro does not
> match (H13 - HB1)
> Warning: atom name 20 in topol.top and box_prot_oct_sol.gro does not
> match (C7 - HB2)
> Warning: atom name 21 in topol.top and box_prot_oct_sol.gro does not
> match (H14 - CG)
> Warning: atom name 22 in topol.top and box_prot_oct_sol.gro does not
> match (H15 - HG)
> Warning: atom name 23 in topol.top and box_prot_oct_sol.gro does not
> match (C8 - CD1)
> (more than 20 non-matching atom names)
>
> WARNING 1 [file topol.top, line 55]:
> 28782 non-matching atom names
> atom names from topol.top will be used
> atom names from box_prot_oct_sol.gro will be ignored
>
> The order of atoms in coordinate file and order of [molecules]
> directive are same.
If that were true, you wouldn't be getting this error. Check your files very
carefully. Something doesn't line up.
-Justin
> I have checked on the gromacs forum and also the documentation but not
> able to rectify the problem.
>
>
>
> This is how I included the octane topology in .top file
> #########################################
> ; Include forcefield parameters
> #include "amber99sb-ildn.ff/forcefield.itp"
> #include "oct.itp"
>
> ; Include chain topologies
> #include "topol_Protein_chain_A.itp"
> #include "topol_Ion_chain_A2.itp"
>
> ; Include water topology
> #include "amber99sb-ildn.ff/tip3p.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
> ; Include topology for ions
> #include "amber99sb-ildn.ff/ions.itp"
>
> [ system ]
> ; Name
> Protein in water
>
> [ molecules ]
> ; Compound #mols
> Protein_chain_A 1
> Ion_chain_A2 1
> SOL 565
> 1-octanol 1
> SOL 8422
> ####################################
>
> Please provide suggestions.
>
> On Tue, Mar 27, 2012 at 17:59, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> bipin singh wrote:
>>> Thanks for your inputs.
>>> I have followed your suggestion and included the .itp for the octane
>>> molecule (containing atomtype definition for new atoms) in the
>>> topology file(.top) of the whole system (prot+oct+water). but during
>>> grompp it produce error and results in termination due to non matching
>>> numbers (27 atoms of octane molecule) between coordinate file and
>>> topology file.
>>>
>>>
>>>
>>> WARNING 1 [file 111-87-5.top, line 15]:
>>> Overriding atomtype h1
>>>
>>>
>>> WARNING 2 [file 111-87-5.top, line 17]:
>>> Overriding atomtype c3
>>>
>>>
>>> WARNING 3 [file 111-87-5.top, line 19]:
>>> Overriding atomtype ho
>>>
>> It appears that you have somehow duplicated atom types and they are
>> overriding each other.
>>
>>
>>> Generated 4656 of the 4656 non-bonded parameter combinations
>>> Generating 1-4 interactions: fudge = 0.5
>>> Generated 4656 of the 4656 1-4 parameter combinations
>>> Excluding 3 bonded neighbours molecule type '1-octanol'
>>> Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
>>> Excluding 3 bonded neighbours molecule type 'Ion_chain_A2'
>>> Excluding 3 bonded neighbours molecule type '1-octanol'
>>> Excluding 2 bonded neighbours molecule type 'SOL'
>>> Excluding 2 bonded neighbours molecule type 'SOL'
>>>
>>> NOTE 1 [file topol.top, line 55]:
>>> System has non-zero total charge: -9.999989e-01
>>>
>>> Program grompp, VERSION 4.5.3
>>> Source code file: grompp.c, line: 523
>>>
>>> Fatal error:
>>> number of coordinates in coordinate file (box_oct_sol.gro, 54297)
>>> does not match topology (topol.top, 54324)
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>>
>>>
>> Did you follow the link? Surely you would have found:
>>
>> http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
>>
>> -Justin
>>
>>
>>> ######################################################################3
>>> this is how I included the itp for the octane molecule in .top file
>>>
>>> ; Include forcefield parameters
>>> #include "amber99sb-ildn.ff/forcefield.itp"
>>> #include "octane.itp"
>>>
>>> ; Include chain topologies
>>> #include "topol_Protein_chain_A.itp"
>>> #include "topol_Ion_chain_A2.itp"
>>>
>>> ; Include water topology
>>> #include "amber99sb-ildn.ff/tip3p.itp"
>>>
>>> #ifdef POSRES_WATER
>>> ; Position restraint for each water oxygen
>>> [ position_restraints ]
>>> ; i funct fcx fcy fcz
>>> 1 1 1000 1000 1000
>>> #endif
>>>
>>> ; Include topology for ions
>>> #include "amber99sb-ildn.ff/ions.itp"
>>>
>>> [ system ]
>>> ; Name
>>> Protein in water
>>>
>>> [ molecules ]
>>> ; Compound #mols
>>> Protein_chain_A 1
>>> Ion_chain_A2 1
>>> 1-octanol 1
>>> SOL 565
>>> SOL 8495
>>> #########################################################################
>>>
>>> -------------------------------------------------------
>>>
>>> Please provide your comments.
>>>
>>> On Tue, Mar 27, 2012 at 03:20, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>> bipin singh wrote:
>>>>> Thanks for your reply.
>>>>>
>>>>> Yes, you are right that these topologies are self supporting and there
>>>>> is no need to to call any other information. I followed your
>>>>> suggestions and able to generate a biphasic system of water/octane
>>>>> containing a protein molecule. But, when I tried grompp on this
>>>>> biphasic system (containing octane+water+protein), it results in error
>>>>> even if I include the topologies in forcefield.itp file.
>>>>>
>>>>> The error was
>>>>>
>>>>> Fatal error:
>>>>> Atomtype hc not found
>>>>> For more information and tips for troubleshooting, please check the
>>>>> GROMACS
>>>>> website at http://www.gromacs.org/Documentation/Errors
>>>>>
>>>> If you introduce a new atomtype in your topology somewhere (presumably in
>>>> one of the GAFF topologies), then you have to declare them in an
>>>> [atomtypes]
>>>> directive in the appropriate place in the .top file. These types are
>>>> case
>>>> sensitive as well. For dealing with GAFF-type topologies, assuming you
>>>> can
>>>> #include them within whatever AMBER force field you've chosen (up to you
>>>> to
>>>> prove), you can do something like:
>>>>
>>>> #include "amberXX.ff/forcefield.itp"
>>>>
>>>> #include "ligand.itp"
>>>>
>>>> [ moleculetype ]
>>>> ;name nrexcl
>>>> Protein 3
>>>>
>>>> (etc)
>>>>
>>>> The inclusion of the ligand topology (at this specific location) will add
>>>> the new [atomtypes] at the appropriate level of precedence, before any
>>>> [moleculetypes] are declared.
>>>>
>>>>
>>>> -Justin
>>>>
>>>>> On Mon, Mar 26, 2012 at 18:46, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>>>>>
>>>>>> bipin singh wrote:
>>>>>>> Thanks for your reply.
>>>>>>> But as far as I understood, in order to use these GAFF topology (for
>>>>>>> e.g. to perform simulation using these topologies) with Gromacs we
>>>>>>> have to incorporate the information from these topologies to the
>>>>>>> existing Amber forcefields in Gromacs or Is there anyway (Possibility
>>>>>>> of using Standalone GAFF parameters in Gromacs) to do it without
>>>>>>> performing this task.
>>>>>>>
>>>>>> As David said, the topologies stand on their own. You do not need to
>>>>>> call
>>>>>> any further information from anywhere. The .top that you downloaded
>>>>>> begins
>>>>>> with a [defaults] directive, declares atom types, and proceeds through
>>>>>> the
>>>>>> rest of the topology with explicit parameters.
>>>>>>
>>>>>>
>>>>>>> As you said these topologies are self supporting and we do not need to
>>>>>>> change ffbonded.itp, but during grompp I got the following error, may
>>>>>>> be because I have not added the dihedral information.
>>>>>>>
>>>>>>> ERROR [file oct.top]:
>>>>>>> No default Proper Dih. types
>>>>>>>
>>>>>>> Please provide your suggestions.
>>>>>>>
>>>>>> I certainly don't see how this could have happened. All the dihedral
>>>>>> parameters are listed explicitly. The fatal error should have printed
>>>>>> a
>>>>>> line number in the .top that is problematic, so start by investigating
>>>>>> there. If you have modified the topology in any way, then undo the
>>>>>> changes
>>>>>> and try again.
>>>>>>
>>>>>> I did not have any trouble using this .top in an unmodified form, so I
>>>>>> suspect you've altered it in some way that has broken it.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>
>>>>>>> On Mon, Mar 26, 2012 at 17:29, David van der Spoel
>>>>>>> <spoel at xray.bmc.uu.se>
>>>>>>> wrote:
>>>>>>>> On 2012-03-26 13:55, bipin singh wrote:
>>>>>>>>> Hello all,
>>>>>>>>>
>>>>>>>>> I am using the GAFF topology provided for octan-1-ol at Gromacs
>>>>>>>>> liquid
>>>>>>>>> database (http://virtualchemistry.org/molecules/111-87-5/index.php).
>>>>>>>>> I
>>>>>>>>> have incorporated all the parameters
>>>>>>>>> for atoms, bonds and non-bonded interaction type in the forcefield
>>>>>>>>> (Amber99sb-ildn in Gromacs) from GAFF topology (111-87-5.top), but
>>>>>>>>> I
>>>>>>>>> am not sure how to add the dihedraltypes information in ffbonded.itp
>>>>>>>>> from the GAFF topology as to add this information I need the phase
>>>>>>>>> and
>>>>>>>>> kd for each dihedral. Is this information is available in the GAFF
>>>>>>>>> topology provided in the Gromacs database ?
>>>>>>>>>
>>>>>>>>>
>>>>>>>> This topology is self supporting and you do not need anything else in
>>>>>>>> ffbonded.itp.
>>>>>>>>
>>>>>>>> You should be careful merging such parameters with an existing force
>>>>>>>> field,
>>>>>>>> because strictly speaking these are different force fields.
>>>>>>>>>
>>>>>>>>>
>>>>>>>> --
>>>>>>>> David van der Spoel, Ph.D., Professor of Biology
>>>>>>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>>>>>>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
>>>>>>>> spoel at xray.bmc.uu.se http://folding.bmc.uu.se
>>>>>>>> --
>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>>> Please search the archive at
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>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> --
>>>>>> ========================================
>>>>>>
>>>>>> Justin A. Lemkul
>>>>>> Ph.D. Candidate
>>>>>> ICTAS Doctoral Scholar
>>>>>> MILES-IGERT Trainee
>>>>>> Department of Biochemistry
>>>>>> Virginia Tech
>>>>>> Blacksburg, VA
>>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>>>
>>>>>> ========================================
>>>>>>
>>>>>> --
>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>>>>>
>>>>>
>>>>>
>>>> --
>>>> ========================================
>>>>
>>>> Justin A. Lemkul
>>>> Ph.D. Candidate
>>>> ICTAS Doctoral Scholar
>>>> MILES-IGERT Trainee
>>>> Department of Biochemistry
>>>> Virginia Tech
>>>> Blacksburg, VA
>>>> jalemkul[at]vt.edu | (540) 231-9080
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
>>>> --
>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>
>>>
>>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>> --
>> gmx-users mailing list gmx-users at gromacs.org
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>
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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