Dear Rajbinder,
As David and Bill said there is no need to modify frcmod.ff14SB to add new (or missing) parameters to the force field. I recommend you to see how FFPTM is implemented on AMBER [
http://selene.princeton.edu/FFPTM]
In practical terms I'd use this kind of leap input file:
# Load AMBER force field
source leaprc.protein.ff14SB
# Load custom parameters
loadOff gamma-coo-GLU.lib
loadAmberParams gamma-coo-GLU.frcmod
Where gamma-coo-GLU.lib is the library containing the residue topology, it can also be a prep file, in which case the command is "loadAmberPrep gamma-coo-GLU.prep"...
gamma-coo-GLU.frcmod is the parameter file containing the following sections [
http://ambermd.org/FileFormats.php#frcmod]:
remark goes here
ANGLE
O2-C -N 72.7 120.63
IMPR
CT-O2-C-N 10.5 180. 2.
In that way you are sure to preserve the original ff14SB parameters
Something I can't understand is the way you are linking the gamma-carboxyglutamic acid to other amino acids in the chain... it seems you are joining the OXT (carboxylic group of the side chain) to the peptide backbone of the next residue instead of joining the peptide backbones... that seems rare to me but I know anything about your system... Any way, as I mentioned in a mail before, the .lib format allows you to set the head and tail linking atom, so the bonds in residue chains can be generated automatically without the need for a bond command see the documentation at AMBER web page [
http://ambermd.org/doc/OFF_file_format.txt]... I guess you can set kind of similar things in prep files but I'm not used to use them...
Best,
Matias
----- Mensaje original -----
De: "Bill Ross" <ross.cgl.ucsf.edu>
Para: amber.ambermd.org
Enviados: Miércoles, 31 de Octubre 2018 6:30:25
Asunto: Re: [AMBER] tleap gamma-carboxyglutamic acid linkage error
Coming on this cold with a Sherlock Holmes approach and vestigial
awareness of chemistry (i.e. Dave's issue and your response), an obvious
possibility is that the frcmod.ff14SB file you added the params to is
not the one you are loading. Try listing the param in leap, or some
addition or deletion experiment to prove to yourself that you are
loading the right file, then burn this message and fly into the night. :-)
Bill
On 10/31/18 2:13 AM, Rajbinder Kaur Virk wrote:
> Hello
>
> This missing parameters is probably due the presence of gamma glutamic acid
> as one of the amino acid in the peptide and it is forming a gamma linkage
> as peptide bond. As discussed earlier, I tried to make .lib file, after
> saving by xleap, the pdb seems to be right but prmtop and inpcrd files are
> not being saved.
>
> Following changes were made in the frcmod.ff14SB file:
> Angle
> O2-C -N 72.7 120.63
> IMPR
> CT-O2-C-N 10.5 180. 2.
>
> Please provide some suggestions....we are really stuck. Thank you
>
> Thank you
> With regards
> Rajbinder Kaur Virk
>
>
> On Wed, Oct 31, 2018 at 7:11 AM David Case <david.case.rutgers.edu> wrote:
>
>> On Tue, Oct 30, 2018, Rajbinder Kaur Virk wrote:
>>> Could not find angle parameter: O2 - C - N
>>>
>>> thereafter i tried to provide the required parameters in the .dat file
>>> itself (frcmod.ff14SB), still the parameter are not being recognized and
>>> the error persists.
>> Can you show the exact changes to the frcmod.ff14SB file you made, plus all
>> the commands you gave to tleap?
>>
>> As an aside, you should generally not edit frcmod.ff14SB itself, but rather
>> make a new frcmod file--that way you won't mess up other runs that expect
>> to
>> have the un-modified frcmod.ff14SB file.
>>
>> Second aside: there are indeed no O2-C-N angles in ordinary proteins. Are
>> you
>> sure you have correct atom types?
>>
>> ....dac
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Wed Oct 31 2018 - 10:30:02 PDT
