[AMBER] Unable to generate parameters of modified amino acids using LEAP

From: Shankha Banerjee <shankhabanerjee2012.gmail.com>
Date: Mon, 23 Sep 2019 19:34:07 +0530

 Dear Amber users
I have been trying to run simulations (using Amber 18) for my protein
containing a modified amino acid. The N-terminal has a myristic acid
connected to Asp as a modification. I added connecting bond to it by using
the leap bond command:
bond MY.594.cC ASP.1.N
I also changed the atom types for the myristic acid component by matching
with those found in the lipid17.dat and lipid17.lib files. When I run leap
now (using the command tleap -s -f leap_g.in), I am getting the following
error:
-I: Adding /home/suchetana/amber18/dat/leap/prep to search path.
-I: Adding /home/suchetana/amber18/dat/leap/lib to search path.
-I: Adding /home/suchetana/amber18/dat/leap/parm to search path.
-I: Adding /home/suchetana/amber18/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source leap_g.in.

Welcome to LEaP!
Sourcing: ./leap_g.in
----- Source: /home/suchetana/amber18/dat/leap/cmd/leaprc.protein.ff14SB
----- Source of /home/suchetana/amber18/dat/leap/cmd/leaprc.protein.ff14SB
done
Log file: ./leap.log
Loading parameters: /home/suchetana/amber18/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /home/suchetana/amber18/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /home/suchetana/amber18/dat/leap/lib/amino12.lib
Loading library: /home/suchetana/amber18/dat/leap/lib/aminoct12.lib
Loading library: /home/suchetana/amber18/dat/leap/lib/aminont12.lib
----- Source: /home/suchetana/amber18/dat/leap/cmd/leaprc.lipid17
----- Source of /home/suchetana/amber18/dat/leap/cmd/leaprc.lipid17 done
Log file: ./leap.log
Loading parameters: /home/suchetana/amber18/dat/leap/parm/lipid17.dat
Reading title:
AMBER Lipid17 v1.1 Force Field, A. Skjevik, C. Dickson, B. Madej, I.R.
Gould, R.C. Walker*
Loading library: /home/suchetana/amber18/dat/leap/lib/lipid17.lib
----- Source: /home/suchetana/amber18/dat/leap/cmd/leaprc.gaff
----- Source of /home/suchetana/amber18/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /home/suchetana/amber18/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
Loading PDB file: ./try_out.pdb

/home/suchetana/amber18/bin/teLeap: Warning!
Name change in pdb file residue 1 ;
this residue is split into MY and ASP.

/home/suchetana/amber18/bin/teLeap: Note.
1 residues had naming warnings.
Thus, there are split residues;
residue sequence numbers will not correspond to those in the pdb.
-- residue 1: duplicate [ cD] atoms (total 13)

/home/suchetana/amber18/bin/teLeap: Warning!
Atom names in each residue should be unique.
     (Same-name atoms are handled by using the first
      occurrence and by ignoring the rest.
      Frequently duplicate atom names stem from alternate
      conformations in the PDB file.)

Created a new atom named: cC within residue: .R<MY 1>
Created a new atom named: oC within residue: .R<MY 1>
Created a new atom named: cD within residue: .R<MY 1>
  Added missing heavy atom: .R<MY 1>.A<C12 38>
  Added missing heavy atom: .R<MY 1>.A<C13 35>
  Added missing heavy atom: .R<MY 1>.A<C14 32>
  Added missing heavy atom: .R<MY 1>.A<C15 29>
  Added missing heavy atom: .R<MY 1>.A<C16 26>
  Added missing heavy atom: .R<MY 1>.A<C17 23>
  Added missing heavy atom: .R<MY 1>.A<C18 20>
  Added missing heavy atom: .R<MY 1>.A<C19 17>
  Added missing heavy atom: .R<MY 1>.A<C110 14>
  Added missing heavy atom: .R<MY 1>.A<C111 11>
  Added missing heavy atom: .R<MY 1>.A<C112 8>
  Added missing heavy atom: .R<MY 1>.A<C113 5>
  Added missing heavy atom: .R<MY 1>.A<C114 2>
  total atoms in file: 604
  Leap added 44 missing atoms according to residue templates:
       13 Heavy
       31 H / lone pairs
  The file contained 3 atoms not in residue templates
Writing pdb file: try_out_1.pdb

/home/suchetana/amber18/bin/teLeap: Warning!
 Converting C-terminal residue name to PDB format: CALA -> ALA
Checking Unit.

/home/suchetana/amber18/bin/teLeap: Warning!
There is a bond of 14.636845 angstroms between:

/home/suchetana/amber18/bin/teLeap: Warning!
The unperturbed charge of the unit (-1.000001) is not zero.
FATAL: Atom .R<MY 1>.A<cC 41> does not have a type.
FATAL: Atom .R<MY 1>.A<oC 42> does not have a type.
FATAL: Atom .R<MY 1>.A<cD 43> does not have a type.

/home/suchetana/amber18/bin/teLeap: Fatal Error!
Failed to generate parameters

Exiting LEaP: Errors = 1; Warnings = 5; Notes = 1.

I am attaching the input PDB file and the leap_g.in file. Kindly advise.

Thanks,
Shankha Banerjee


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Received on Mon Sep 23 2019 - 07:30:02 PDT
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