Hello,
I tried to build a non standard residue (an azide group that is attaching to a GLY residue) for AMBER using Pyred.
It seems that PyRED is not able to assign the right atom types to Nitrogens in azide group. (two nitrogens with double bonds (one with +1 charge and the other with -1 charge). I attached the figure of ACE-AZA(non standard: Azide)-NME to this email.
These are the unknown parameters in frcmod.unknown
N?
CT-NC
N*-N?
N*-NC
CX-CT-NC
H1-CT-NC
N?-N*-NC
CT-NC-N*
CX-CT-NC-N*
H1-CT-NC-N*
N?-N*-NC-CT
How can I get the right atom types for these atoms? I already tried “
http://www.quimica.urv.es/~bo/MOLMOD/General/Forcefields/AMBER.html#N <
http://www.quimica.urv.es/~bo/MOLMOD/General/Forcefields/AMBER.html#N>” but I can not find these exact atoms types.
How can I get the unknown parameters?
I am not also sure about the hybridization. NC, N* and N? should be all sp as far as I know not sp2.
I also attached the figure, mol2(after atom types are assigned with charges for the central part of ACE-AZA-NME), leaprc.q4mdfft (that I modified), frcmod.unknown and frcmod.known for the AZA to this email.
I appreciate your help.
Best regards,
Maral
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Department of Chemical and Materials Engineering
University of Alberta
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Received on Fri Feb 24 2017 - 09:30:03 PST
