Hi Maximilien,
It looks like you need to use the AmberTools program charmmlipid2amber.py,
to change the lipid residue names and topologies for Amber Lipid14. That
should fix the issue with the lipid residues, which it looks like leap is
reading in as DOP. You also need to adjust the residue name for histidine,
currently being read by leap as HSD. See the following:
http://ambermd.org/Questions/HIS.html.
When you run leap again, you will see warnings about "split residues" for
the lipids, but this is normal behavior for the Amber lipid force field.
Best,
Sally
Sally Pias
New Mexico Tech
On Fri, Apr 19, 2019 at 10:19 AM Maximilien BERNE <
maximilien.berne.etu.univ-nantes.fr> wrote:
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 19 2019 - 12:30:03 PDT
