[AMBER] Fwd: leap error for modified amino acid

From: Ipsita Basu <ibasu788.gmail.com>
Date: Tue, 24 Aug 2021 16:44:12 +0530

Dear all,
I am trying to generate parameters for a protein containing modified
cysteine residue which I named as "CYL". First I run pdb4amber and
then took the output from the non-standard part. It has one nitro
group where N is positively charged and one oxygen is negatively
charged. If I run antechamber using amber then atomtype is set as "DU"
for that oxygen. But using gaff it set all atom types. Then
successfully I have prepared the prepin and frcmod file. But when I
run tleap, it is giving error of missing parameters parameters and
finally parameter file is not saved.
Can you please help me to get rid o this problem?
I am providing the required input files.
Thanks in advance..
Ipsita Basu
Post Doctoral Fellow,

Ipsita Basu
Post Doctoral Fellow,
Dept. of Physics,
IISC, Bangalore

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Received on Tue Aug 24 2021 - 04:30:02 PDT
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