Hello,
There are existing parameters for TPO (and other phosphorylated amino
acids) available for use with ff14SB and ff19SB.
You can source leaprc.phosaa14SB or leaprc.phosaa19SB to use them.
Best,
Lauren Raguette
Simmerling Lab | Stony Brook University
> From: fateme haghighi via AMBER <amber.ambermd.org>
> Date: Thu, Mar 20, 2025, 12:23 PM
> Subject: [AMBER] modified amino acid residue error while using antechamber
> To: amber.ambermd.org <amber.ambermd.org>, amber-request.ambermd.org <
> amber-request.ambermd.org>, amber-owner.ambermd.org <
> amber-owner.ambermd.org>
>
>
>
>
> Hi,
> I am following *tutorial B5 ("Simulating the Green Fluorescent
> **Protein")to build parameters for phosphorylated threonine (TPO).
> I used following code:
> antechamber -fi ccif -i TPO.cif -bk TPO -fo ac -o TPO.ac -c bcc -at amber
>
> but I got the following error.*
>
> amber24_src/AmberTools/src/antechamber/mmcif.c:65: rmmcif: Assertion `col6
> >= 0' failed.
> /home/amber24/bin/antechamber: line 9: 46194 Aborted (core
> dumped) "$AMBERHOME/bin/wrapped_progs/antechamber" "$@"
>
> I could not attach the cif file. Please tell me how to resolve the error.
>
> Thanks in advance.
>
>
>
>
>
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Received on Thu Mar 20 2025 - 10:30:02 PDT
