Dear AMBER developers,
I recently encountered a strange combination of files, unit names for
non-standard residues that did not cause an error in tleap and successfully
generated prmtop/inpcrd files, even though I expected a crash for the
following reasons.
Thus, I want to confirm if all is well in the files and simulation or if
there is a bug in AmberTools that needs fixing. I'm using Amber22 on this
GPU workstation.
The situation is the following.
I have protein, cofactor and ligand in the system.
I generated mol2 and frcmod files using antechamber for both cofactor and
the ligand, and I accidently kept the residue name 'MOL' the same for both
in the respective mol2 files.
Now when I ran the following tleap command, it didn't produce any errors
and even a few steps of the production run proceeded successfully.
I assume the standard practice requires a unique residue name for all
unique residues (standard or non-standard). Furthermore, for non-standard
ligands, these names should match between the mol2 files and the complex
PDB for atom-types and charges.
Any mismatch can lead to multiple charges being used for same atom types in
a residue and thus should result in errors while generating prmtop/inpcrd
files.
I'm requesting the developers/experts to confirm this and explain why it
didn't produce the expected error and generated prmtop/inpcrd files anyways.
tleap file, where the same residue names are used for the ligand and
cofactor inside the mol2 files.
source leaprc.protein.ff14SB
source leaprc.gaff
source leaprc.water.tip3p
loadamberparams ligand.frcmod
loadamberparams cofactor.frcmod
PROT = loadpdb protein_amber.pdb
MOL = loadmol2 ligand.mol2
COF = loadmol2 cofactor.mol2
COMPLEX = combine { PROT MOL COF }
check COMPLEX
charge COMPLEX
saveamberparm COMPLEX complex_dry.prmtop complex_dry.inpcrd
savepdb COMPLEX complex_dry.pdb
solvatebox COMPLEX TIP3PBOX 12.0
addions COMPLEX Na+ 0
addions COMPLEX Cl- 0
check COMPLEX
charge COMPLEX
saveamberparm COMPLEX complex.prmtop complex.inpcrd
savepdb COMPLEX complex_solvated.pdb
quit
Thank you and best regards,
Vaibhav
Regards,
Dr. Vaibhav A. Dixit,
Asst. Prof., Department of Medicinal Chemistry,
National Institute of Pharmaceutical Education and Research, Guwahati
(NIPER-G), Sila Katamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup, Pin:
781101, Assam, India
Mob. No. +91-7709129400,
Email: vaibhav.niperguwahati.in; vaibhavadixit.gmail.com
https://niperguwahati.ac.in/DOC/profile/dixit.pdf
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
NCBI bibliography:
https://www.ncbi.nlm.nih.gov/myncbi/1Jgo56b26_AYKd/bibliography/public/
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Tue Sep 22 2026 - 05:30:02 PDT
