[gmx-users] Re: How to add dihedral information from the GAFF topology
bipin singh
bipinelmat at gmail.com
Wed Mar 28 00:52:58 CEST 2012
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.
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
>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>> --
>>>>> ========================================
>>>>>
>>>>> 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
>>>
>>> ========================================
>>> --
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>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>
> --
> ========================================
>
> 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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