[gmx-users] Re: How to add dihedral information from the GAFF topology
Justin A. Lemkul
jalemkul at vt.edu
Tue Mar 27 14:29:47 CEST 2012
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
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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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>>>
>>>
>>>
>> --
>> ========================================
>>
>> 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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>
>
>
--
========================================
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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