Greetings,
I have generated the ligand library for my ligand file but it is still not working. I have been following the tutorial for simulating a pharmaceutical compound. The process goes well until the generation of ligand library. When it comes to the complex part, the process gives fatal error showing that there is problem is atom bond order. The error file I am attaching herewith. Please help me with this. I am also attaching the complex file.
Regards,
Simran Modi
-----Original Message-----
From: Dr. Anselm Horn via AMBER <amber.ambermd.org>
Sent: Friday, August 9, 2024 1:43 PM
To: amber.ambermd.org
Subject: Re: [AMBER] Error in ligand paramterisation in tleap
Simran,
it is not clear what exactly you did, since you did not include the actual input pdb file of the complex nor the ligand library you created.
Your error description "trying to edit the atom types used in amber but it is failing" does not allow for specific pieces of advice.
Force field parameterization is an advanced topic; often problems arise from some unfamiliarity with the methodological background. Maybe the tutorials on the Amber website as well as the manual provide you with a sound starting point.
And perhaps there are already force field parameters available for your ligand? Or a chemically similar ligand has been parameterized, and you could build on that knowledge?
>From a practical point of view:
tleap.out tells us that you defined a ligand via ligand.prepi and created additional parameters in ligand.frcmod, presumably using the parm14SB force field. However, your ligand definition in the prepi file does not match the ligand definition in the pdb input file (different unit name/different atom names?) tleap_1.out tells us that you defined a ligand via ligand.prepi and created additional parameters in ligand.frcmod, presumably using the gaff force field. However, your ligand definition in the prepi file does not match the ligand definition in the pdb input file (different atom names); maybe you mixed up atom names and atom types.
-> Your ligand in the input pdb file must have the same residue name and
atom names as in the prepi file, where the ligand is defined. Otherwise this part of the input cannot be assigned any force field parameters, and thus the save command fails. All this in turn depends on the force field you choose to describe the ligand, and thus on the atom types you assign to the ligand atoms and the parameters you use for the molecular description.
Good luck,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Germany
Am 09.08.2024 um 12:23 schrieb Simran Modi via AMBER:
> Greetings,
> I am trying to simulate the protein ligand complex. I am getting errors in building complex in tleap i.e. recognition of atom types. I have been manually trying to edit the atom types used in amber but it is failing. I am hereby attaching the complex along with he error files. Please let me know the solution.
>
> Regards,
> Simran Modi
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Received on Tue Aug 20 2024 - 02:00:02 PDT
