[gmx-users] updating amberff.03 files
Mark Abraham
mark.j.abraham at gmail.com
Fri Apr 12 08:10:21 CEST 2013
On Apr 11, 2013 11:51 PM, "Laura Kingsley" <lkingsle at purdue.edu> wrote:
>
> So if I'm understanding you correctly in the .rtp file under
>
> [ HEME ]
> [ dihedrals ]
>
> I should change:
> HP42 CBD CGD O1D
> HP42 CBD CGD O2D
> ...
>
> to
>
> HP42 CBD CGD O1D 3 0.65270 1.95811 0.00000 -2.61082
0.00000 0.00000
> HP42 CBD CGD O2D 3 0.65270 1.95811 0.00000 -2.61082
0.00000 0.00000
I believe so.
>
>
> Do I need to remove these definitions from the ffbonded.itp files then?
Unused entries do no harm.
Mark
>
> - Laura
>
>
>
> On 04/11/2013 05:43 PM, Mark Abraham wrote:
>>
>> On Thu, Apr 11, 2013 at 11:14 PM, Laura Kingsley<lkingsle at purdue.edu
>wrote:
>>
>>> Hi Mark,
>>>
>>> We'd like to use the Ryckaert-Bellemans dihedral types. Does 3 not work
in
>>> the new version?
>>
>>
>> Sorry, I was thinking of 4 and 9, which are basically interchangeable.
The
>> default for AMBER did change to 9 at some point (see top of
>> aminoacids.rtp). You can use the old approach if you change the types of
>> just the heme dihedrals to 3 in the .itp files produced by pdb2gmx. Or
you
>> can probably edit the heme .rtp entry to specify type 3 (plus parameters,
>> perhaps via the #defines).
>>
>> Also, I took out the #define lines and replaced them with the actual
>>>
>>> atomtypes, because that didn't seem to work when I initially tried to
add
>>> just the #define lines to the ffbonded.itp file.
>>
>>
>> The parameters need to go either on the lines in the .rtp that define the
>> interactions, or on the lines that define the dihedraltypes. Only the
>> latter needs the atom types (because that's how the lookup works). The
>> old-style #defines cannot work in ffbonded.itp, because they assume the
>> context of the .rtp, where the atoms are already identified.
>>
>> Mark
>>
>>
>>>
>>> On 04/11/2013 04:51 PM, Mark Abraham wrote:
>>>
>>>> Type 9 was added at some point to GROMACS to make coping with AMBER and
>>>> CHARMM easier. So you should just change your #defines from 3 to 9. See
>>>> table in chapter 5. Or you could just leave your solution in the same
form
>>>> as you did for the 4.0.x GROMACS.
>>>>
>>>> Mark
>>>>
>>>>
>>>> On Thu, Apr 11, 2013 at 10:36 PM, Laura Kingsley<lkingsle at purdue.edu>**
>>>> wrote:
>>>>
>>>> Hello Gromacs Users,
>>>>>
>>>>>
>>>>> I am trying to update the contents of the top folder. I have
parameters
>>>>> for a HEME residue that worked in gromacs 4.0.7, and we're now trying
to
>>>>> update to gromacs 4.6.1 (long overdue), and need to migrate the
>>>>> parameters
>>>>> over to the new version.
>>>>>
>>>>> I have done the following:
>>>>>
>>>>> 1. added the HEME atomtypes to the atomtypes.atp file
>>>>> 2. added the hydrogens to the aminoacids.hdb file
>>>>> 3. added the [ HEME ] block to the aminoacids.rtp file
>>>>>
>>>>>
>>>>> I am running into problems in adding the dihedrals. in the old
version we
>>>>> had used #define statements in the ffamber03bon.itp file
(ffbonded.itp
>>>>> in
>>>>> the 4.6 version) , for example:
>>>>>
>>>>> #define heme_1 0.00000 0.00000 0.00000 0.00000
>>>>> 0.00000 0.00000
>>>>> #define heme_2 0.62760 1.88280 0.00000 -2.51040
>>>>> 0.00000 0.00000
>>>>> #define heme_3 0.65270 1.95811 0.00000 -2.61082
>>>>> 0.00000 0.00000
>>>>> #define heme_4 16.52680 0.00000 -16.52680 0.00000
>>>>> 0.00000 0.00000
>>>>> #define heme_5 62.76000 0.00000 -62.76000 0.00000
>>>>> 0.00000 0.00000
>>>>>
>>>>>
>>>>> the "heme_X" term was defined in the ffamber03.rtp file
(aminoacids.rtp
>>>>> file in ver 4.6)- for example:
>>>>>
>>>>> [ dihedrals ]
>>>>> HP42 CBD CGD O1D heme_1
>>>>> HP42 CBD CGD O2D heme_1
>>>>> HP41 CBD CGD O1D heme_1
>>>>> HP41 CBD CGD O2D heme_1
>>>>> HP52 CAD CBD HP41 heme_2
>>>>> HP52 CAD CBD HP42 heme_2
>>>>> HP52 CAD CBD CGD heme_3
>>>>>
>>>>>
>>>>>
>>>>> I updated all "define heme_X" lines in the ffbonded.itp file by going
>>>>> back and putting in the actual atomtypes and the corresponding
dihedral
>>>>> function and parameters. For example:
>>>>>
>>>>> I replaced
>>>>> #define heme_8 11.92440 0.00000 -11.92440 0.00000
>>>>> 0.00000 0.00000
>>>>>
>>>>> with :
>>>>> FE NO CC CD 3 11.92440 0.00000 -11.92440 0.00000
>>>>> 0.00000 0.00000
>>>>>
>>>>>
>>>>>
>>>>> However, I'm getting errors from the grompp command about the
dihedrals.
>>>>> it gives:
>>>>>
>>>>> ERROR 1 [file prot_Other_chain_B2.itp, line 520]:
>>>>> No default Proper Dih. types
>>>>>
>>>>>
>>>>> ERROR 2 [file prot_Other_chain_B2.itp, line 521]:
>>>>> No default Proper Dih. types
>>>>> .
>>>>> .
>>>>> .
>>>>>
>>>>>
>>>>> I'm thinking that it can't find the Dihedral types that I added t the
>>>>> ffbonded.itp file, but I'm not sure why. One thing I've noticed is
that
>>>>> in
>>>>> the .itp file generated by pdb2gmx the dihedral type for the heme is
>>>>> given
>>>>> as a 9, but in the ffbonded.itp file, I specify it as a 3. I'm not
sure
>>>>> where its reading this from.
>>>>>
>>>>> I'm hoping that this is just a simple thing that I'm missing and
someone
>>>>> can help point me in the right direction.
>>>>>
>>>>>
>>>>> Thanks,
>>>>>
>>>>> - Laura
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Laura Kingsley
>>>>>
>>>>> Graduate Student
>>>>> Medicinal Chemistry and Molecular Pharmacology
>>>>> Purdue University
>>>>> Office: RHPH 504A
>>>>> 575 Stadium Mall Dr.
>>>>> West Lafayette, IN 47907
>>>>> Office Phone: (765) 496-6643
>>>>>
>>>>> --
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>>> --
>>> Laura Kingsley
>>>
>>> Graduate Student
>>> Medicinal Chemistry and Molecular Pharmacology
>>> Purdue University
>>> Office: RHPH 504A
>>> 575 Stadium Mall Dr.
>>> West Lafayette, IN 47907
>>> Office Phone: (765) 496-6643
>>>
>>> --
>>> gmx-users mailing list gmx-users at gromacs.org
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>
> --
> Laura Kingsley
>
> Graduate Student
> Medicinal Chemistry and Molecular Pharmacology
> Purdue University
> Office: RHPH 504A
> 575 Stadium Mall Dr.
> West Lafayette, IN 47907
> Office Phone: (765) 496-6643
>
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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