[gmx-users] Re: How to add dihedral information from the GAFF topology
bipin singh
bipinelmat at gmail.com
Tue Mar 27 10:43:51 CEST 2012
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
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
######################################################################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
>>>
>>> ========================================
>>>
>>> --
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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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--
-----------------------
Regards,
Bipin Singh
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