Hello,
1. I am making a non-standard residue. I used RED software to get the charges and unknown parameters (the mol2 file is attached). Since I can not find the parameters that I needed from parm99.dat, I want to give hybrid gaff and parm99.dat a try. I attached the figure of the non-standard residue to this post. The non-standard residue is an azide group attached to ALA residue.
2. We have three N with two double bonds and sp hybridization.
I checked the gaff.dat file and I chose (n1 14.01 0.530 Sp N) for my nitrogens. I added
addAtomTypes {
> { "n1" "N" "sp” }
to my leaprc.q4mdfft script attached here as .
3. But when I try to make the lib file, the hybridization changed to sp2 because all the carbon types in leaprc.gaff are sp2 and it gave me this error: atom type n1 - unknown hybridization sp.
Why there is discrepancy between gaff.dat and leaprc.gaff hybridization of different atomtypes? How can I fix it?
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 Mon Mar 13 2017 - 13:30:02 PDT
