[AMBER] trouble in amberFATA: Atom doesn't have a type

From: Maximilien BERNE <maximilien.berne.etu.univ-nantes.fr>
Date: Fri, 19 Apr 2019 18:19:14 +0200 (CEST)

Dear AMBERs,

I hope everything is fine for you
I'm new in working with Amber. Actually using AMBER 16. And I got a
probleme that i hope you could help me solve.

So i try to make a MD on a protein with a lipid bilayer structure (created
with CHARMM-GUI).
i succed on creating this bilayer strucutre , and with the help of your
tutorial ( http://ambermd.org/tutorials/advanced/tutorial16/index.html), i
succesfully added part( 1 alpha-helice) of my proteins in the membrane .

Then i added the rest of my proteins with pymol on this helice so that my
protein could be completed.

And now i try to make a MD of this system.
I followed your manual AMBER 2018 to prepare my PDB
-removing all hydrogen
-putting TER between everything that doesn't have covalent bond (like lipid)
-Delete all water.

BUT here's my problem :

when i try to add this complex in tleap it failed to generate parametre :

Welcome to LEaP!
(no leaprc in search path)
> source leaprc.protein.ff14SB
----- Source:
/comptes/usr/local/opt/apps/pkg/18.04/amber/16/dat/leap/cmd/leaprc.protein.ff14SB
----- Source of
/comptes/usr/local/opt/apps/pkg/18.04/amber/16/dat/leap/cmd/leaprc.protein.ff14SB
done
Log file: ./leap.log
Loading parameters:
/comptes/usr/local/opt/apps/pkg/18.04/amber/16/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters:
/comptes/usr/local/opt/apps/pkg/18.04/amber/16/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library:
/comptes/usr/local/opt/apps/pkg/18.04/amber/16/dat/leap/lib/amino12.lib
Loading library:
/comptes/usr/local/opt/apps/pkg/18.04/amber/16/dat/leap/lib/aminoct12.lib
Loading library:
/comptes/usr/local/opt/apps/pkg/18.04/amber/16/dat/leap/lib/aminont12.lib
> source leaprc.lipid14
----- Source:
/comptes/usr/local/opt/apps/pkg/18.04/amber/16/dat/leap/cmd/leaprc.lipid14
----- Source of
/comptes/usr/local/opt/apps/pkg/18.04/amber/16/dat/leap/cmd/leaprc.lipid14
done
Log file: ./leap.log
Loading parameters:
/comptes/usr/local/opt/apps/pkg/18.04/amber/16/dat/leap/parm/lipid14.dat
Reading title:
AMBER Lipid14 Force Field, C. Dickson, B. Madej, A.Skjevik, K. Teigen,
I.R. Gould, R.C. Walker*
Loading library:
/comptes/usr/local/opt/apps/pkg/18.04/amber/16/dat/leap/lib/lipid14.lib
> loadamberparams frcmod.ionsjc_tip3p
Loading parameters:
/comptes/usr/local/opt/apps/pkg/18.04/amber/16/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
JPCB (2008)
> term = loadpdb term.pdb

#after that i got a HUGE list

Creating new UNIT for residue: DOP sequence: 349
Starting new chain with
Created a new atom named: N within residue: .R<DOP 349>
Created a new atom named: P within residue: .R<DOP 349>
Created a new atom named: C1 within residue: .R<DOP 349>
Created a new atom named: C2 within residue: .R<DOP 349>
Created a new atom named: C3 within residue: .R<DOP 349>
Created a new atom named: C11 within residue: .R<DOP 349>
Created a new atom named: O11 within residue: .R<DOP 349>
Created a new atom named: C12 within residue: .R<DOP 349>
[...]
Created a new atom named: C313 within residue: .R<DOP 349>
Created a new atom named: C314 within residue: .R<DOP 349>
Created a new atom named: C315 within residue: .R<DOP 349>
Created a new atom named: C316 within residue: .R<DOP 349>
Created a new atom named: C317 within residue: .R<DOP 349>
Created a new atom named: C318 within residue: .R<DOP 349>
One sided connection. Residue: default_name missing connect1 atom.
Joining ASN - ALA
Joining ALA - ALA
Joining ALA - ALA
Joining ALA - GLU
Joining GLU - SER
Joining SER - ARG
Joining ARG - LYS
Joining LYS - GLY
Joining GLY - GLN
Joining GLN - GLU
Joining GLU - ARG
Joining ARG - LEU
Joining LEU - GLU
Creating new UNIT for residue: HSD sequence: 364
One sided connection. Residue: missing connect0 atom.
Created a new atom named: N within residue: .R<HSD 364>
Created a new atom named: CA within residue: .R<HSD 364>
Created a new atom named: C within residue: .R<HSD 364>
Created a new atom named: O within residue: .R<HSD 364>
Created a new atom named: CB within residue: .R<HSD 364>
Created a new atom named: CG within residue: .R<HSD 364>
Created a new atom named: CD2 within residue: .R<HSD 364>
Created a new atom named: ND1 within residue: .R<HSD 364>
Created a new atom named: CE1 within residue: .R<HSD 364>
Created a new atom named: NE2 within residue: .R<HSD 364>
Creating new UNIT for residue: HSD sequence: 365
Starting new chain with

#for all my residue ending at

Created a new atom named: OT2 within residue: .R<HSD 377>
  total atoms in file: 11885
  Leap added 1314 missing atoms according to residue templates:
       1 Heavy
       1313 H / lone pairs
  The file contained 10489 atoms not in residue templates

# but the residue are DOPC which are created byt Charmm-GUI.
#And if i try to generate parameter file (which is my objective)
> saveamberparm term term.prmtop term.inpcrd
Checking Unit.

WARNING: The unperturbed charge of the unit: -13.000000 is not zero.
FATAL: Atom .R<DOP 158>.A<N 1> does not have a type.
FATAL: Atom .R<DOP 158>.A<P 2> does not have a type.
FATAL: Atom .R<DOP 158>.A<C1 3> does not have a type.
FATAL: Atom .R<DOP 158>.A<C2 4> does not have a type.
FATAL: Atom .R<DOP 158>.A<C3 5> does not have a type.
FATAL: Atom .R<DOP 158>.A<C11 6> does not have a type.
FATAL: Atom .R<DOP 158>.A<O11 7> does not have a type.
FATAL: Atom .R<DOP 158>.A<C12 8> does not have a type.
FATAL: Atom .R<DOP 158>.A<O12 9> does not have a type.
FATAL: Atom .R<DOP 158>.A<C13 10> does not have a type.
FATAL: Atom .R<DOP 158>.A<O13 11> does not have a type.
FATAL: Atom .R<DOP 158>.A<C14 12> does not have a type.
FATAL: Atom .R<DOP 158>.A<O14 13> does not have a type.
FATAL: Atom .R<DOP 158>.A<C15 14> does not have a type.
FATAL: Atom .R<DOP 158>.A<C21 15> does not have a type.
FATAL: Atom .R<DOP 158>.A<O21 16> does not have a type.
FATAL: Atom .R<DOP 158>.A<C22 17> does not have a type.
FATAL: Atom .R<DOP 158>.A<O22 18> does not have a type.
FATAL: Atom .R<DOP 158>.A<C23 19> does not have a type.
FATAL: Atom .R<DOP 158>.A<C24 20> does not have a type.
FATAL: Atom .R<DOP 158>.A<C25 21> does not have a type.
FATAL: Atom .R<DOP 158>.A<C26 22> does not have a type.
FATAL: Atom .R<DOP 158>.A<C27 23> does not have a type.
FATAL: Atom .R<DOP 158>.A<C28 24> does not have a type.
FATAL: Atom .R<DOP 158>.A<C29 25> does not have a type.
FATAL: Atom .R<DOP 158>.A<C31 26> does not have a type.
FATAL: Atom .R<DOP 158>.A<O31 27> does not have a type.
FATAL: Atom .R<DOP 158>.A<C32 28> does not have a type.
FATAL: Atom .R<DOP 158>.A<O32 29> does not have a type.
FATAL: Atom .R<DOP 158>.A<C33 30> does not have a type.
FATAL: Atom .R<DOP 158>.A<C34 31> does not have a type.
FATAL: Atom .R<DOP 158>.A<C35 32> does not have a type.
FATAL: Atom .R<DOP 158>.A<C36 33> does not have a type.
FATAL: Atom .R<DOP 158>.A<C37 34> does not have a type.
FATAL: Atom .R<DOP 158>.A<C38 35> does not have a type.
FATAL: Atom .R<DOP 158>.A<C39 36> does not have a type.
FATAL: Atom .R<DOP 158>.A<C210 37> does not have a type.
[...]
FATAL: Atom .R<HSD 376>.A<CG 6> does not have a type.
FATAL: Atom .R<HSD 376>.A<CD2 7> does not have a type.
FATAL: Atom .R<HSD 376>.A<ND1 8> does not have a type.
FATAL: Atom .R<HSD 376>.A<CE1 9> does not have a type.
FATAL: Atom .R<HSD 376>.A<NE2 10> does not have a type.
FATAL: Atom .R<HSD 377>.A<N 1> does not have a type.
FATAL: Atom .R<HSD 377>.A<CA 2> does not have a type.
FATAL: Atom .R<HSD 377>.A<C 3> does not have a type.
FATAL: Atom .R<HSD 377>.A<CB 4> does not have a type.
FATAL: Atom .R<HSD 377>.A<CG 5> does not have a type.
FATAL: Atom .R<HSD 377>.A<CD2 6> does not have a type.
FATAL: Atom .R<HSD 377>.A<ND1 7> does not have a type.
FATAL: Atom .R<HSD 377>.A<CE1 8> does not have a type.
FATAL: Atom .R<HSD 377>.A<NE2 9> does not have a type.
FATAL: Atom .R<HSD 377>.A<OT1 10> does not have a type.
FATAL: Atom .R<HSD 377>.A<OT2 11> does not have a type.
Failed to generate parameters
Parameter file was not saved.
> quit


help me Mr(s) AMBER you're my only hope


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Received on Fri Apr 19 2019 - 09:30:02 PDT
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