[gmx-users] updating amberff.03 files

[Mark Abraham]

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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