[gmx-users] updating amberff.03 files

Laura Kingsley lkingsle at purdue.edu
Thu Apr 11 23:51:01 CEST 2013 

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


Do I need to remove these definitions from the ffbonded.itp files then?

- 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

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