[gmx-users] updating amberff.03 files

[Laura Kingsley]

Hi Mark,

We'd like to use the Ryckaert-Bellemans dihedral types. Does 3 not work 
in the new version? 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.



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
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>

-- 
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