Hi,
You might want to try the 'prepareforleap' command in cpptraj, since
one of the functions is to assign correct Glycam names for sugars. Try
something like the following cpptraj input:
parm 1FQ9.pdb
loadcrd 1FQ9.pdb name MyCrd
prepareforleap cricket MyCrd name Prepared pdbout Prepared.pdb
leapunitname Mol out Prepared.leap.in nowat noh
Then you can put something like the following into your leap.in file
(replace with your desired force field files):
source leaprc.protein.ff14SB
source leaprc.GLYCAM_06j-1
source Prepared.leap.in
saveamberparm Mol 1FQ9.parm7 1FQ9.rst7
quit
Then run 'tleap -f leap.in'. Hope this helps,
-Dan
On Fri, Mar 22, 2024 at 6:47 AM SUBHASMITA MAHAPATRA MAHAPATRA via
AMBER <amber.ambermd.org> wrote:
>
> Hello,
>
> I want to simulate this PDB:1FQ9. It has two chains of heparan sulfate
> (E,F). They have this residue 'UAP' and I am unable to find its name as per
> Glycam force field. I have tried the Glycam-web interface.
>
> Kindly help me in this regard.
>
> Thank you
>
> --
> *Yours Sincerely*
> *Subhasmita Mahapatra*
> *Ph.D. Scholar (PMRF)*
> *Computational Biophysics Group*
> *Department of Biosciences and Biomedical Engineering*
> *Indian Institute of Technology, Indore*
> *Madhya Pradesh, India (453552)*
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Received on Fri Mar 22 2024 - 05:30:02 PDT
