Dear All,
I use ambertool( amberchamber tleap) to prepare the parameters of my protein-DNA complex ,which contains one non-standard nucleotide in the middle of chain, I have created and parametrized this nucleotide smoothly ,and I also created an frcmod file and lib file of this nucleotide with parmchk. But when I try to build the prmtop/inpcrd file of my complex after I loaded the prepared frcmod and lib file, tleap complains about missing parameters (angles;bonds;torsion parameters), then I added the relevant parameters to the frcmod file to have tleap to handle the angles and bonds ,but the dihedral parameters can not recognized for encountering fatal error, here I used the learc.ff99SB and learc.gaff ,I googled this problem ,however, I do not undestand completely ,I haved tried the two methods ,1) make the non-standard nucleotide with all Amber atom types (capital letters), or 2)create a frcmod file with the above parameters,probably just using analogous parameters from parm99.dat; both of them failed.
now the error message goes like this :
Building proper torsion parameters.
** No torsion terms for CT-OS-p4-o
** No torsion terms for CT-OS-p4-oh
** No torsion terms for CT-OS-p4-os
** No torsion terms for ho-oh-P-O2
** No torsion terms for ho-oh-P-O2
** No torsion terms for ho-oh-P-OS
** No torsion terms for c3-oh-P-O2
** No torsion terms for c3-oh-P-O2
** No torsion terms for c3-oh-P-OS
Building improper torsion parameters.
How shoul I do?
Thanks for your help!
zhang aidi
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Received on Fri Apr 20 2012 - 11:00:02 PDT
