Hi,
I am trying to parameterize (get .top and .rst7 files) a protein molecule
with a non standard amino acid cysteinyl-flavin (CFN). CFN contains a
covalent bond between C4A of flavin mononucleotide (FMN) and SG of
Cysteine.
I tried antechamber with no success perhaps due to the following reasons
1. pdb4amber or reduce is not adding hydrogens to CFN. Although reducing
other residues in the protein
2. cif file is not available for CFN. Although, the cif file is available
for FMN. So parametrization with antechamber works if I treat CYS (as CYM
(to not reduce SG)) and FMN as separate in the protein pdb. But, doing so
breaks the cysteine- FMN covalent bond during minimization. I want to
retain this bond intact during the simulation. Therefore trying to
parametrize the protein molecule in which CYS and FMN are treated as one
residue CYM.
I have also tried restraining CYM and FMN using strong force constants on
these two, but covalent bond breaks during minimization.
After trying these options I write here to seek help with creating
parameter files for the protein containing CFN residue in AMBER.
Also, like to mention here that parameters for CFN are built and published
using GROMACS. Can we use these or modify these to work in amber?
Thank You,
Amit
--
_
_
*Please consider the environment before printing this email.*
The
information contained in this electronic message and any *attachments to
this message are intended for the exclusive use of addressee(s) and may
contain proprietary, confidential or privileged information. If you are not
the intended recipient, you should not disseminate, distribute **or copy
this e-mail. Please notify the
sender immediately and destroy all copies of
this message and any attachments.***
**
**WARNING***: The recipient should
check this email and any attachments for
the presence of viruses. JMI
accepts no liability for any damage caused by any
virus transmitted by this
email.*
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 28 2020 - 06:00:05 PDT
