Hi Maximilien,
If you could attach the input pdb, that would help. As Callum mentioned,
pdb4amber seems to be the culprit. As the parts of the lipids are
considered residues, TER flags are added where they shouldn't. This is also
the case with tleap, which will add these TER flags to the pdb that comes
out (but not to the output topology file!!!!). This means that once you
process your pdb file once with tleap, if you get a pdb file as output, you
can not process that pdb again with tleap unless you remove the TER flags
in between the lipid residues that make one unit (that is, as an example
OL-PC-OL-TER-OL-PC-OL-TER-....). tleap was not made to handle membrane
systems particularly, and you will get these messages that the lipids are
being split into residues. You can check if your heads and tails are
actually bonded with parmed, like:
parmed -p parmtop_of_your_system
printBonds :PC :OL (or whatever head an tail you are using)
Hope it helps,
El mié., 15 may. 2019 a las 16:19, Maximilien BERNE (<
maximilien.berne.etu.univ-nantes.fr>) escribió:
> Welcome to LEaP!
> (no leaprc in search path)
> > source leaprc.water.tip3p
> ----- Source:
> /comptes/E117951H/amber/amber16/dat/leap/cmd/leaprc.water.tip3p
> ----- Source of
> /comptes/E117951H/amber/amber16/dat/leap/cmd/leaprc.water.tip3p done
> Loading library:
> /comptes/E117951H/amber/amber16/dat/leap/lib/atomic_ions.lib
> Loading library: /comptes/E117951H/amber/amber16/dat/leap/lib/solvents.lib
> Loading parameters:
> /comptes/E117951H/amber/amber16/dat/leap/parm/frcmod.tip3p
> Reading force field modification type file (frcmod)
> Reading title:
> This is the additional/replacement parameter set for SPC/E water
> Loading parameters:
> /comptes/E117951H/amber/amber16/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)
> Loading parameters:
> /comptes/E117951H/amber/amber16/dat/leap/parm/frcmod.ions234lm_126_tip3p
> Reading force field modification type file (frcmod)
> Reading title:
> Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water
> model (12-6 normal usage set)
> > source leaprc.protein.ff14SB
> ----- Source:
> /comptes/E117951H/amber/amber16/dat/leap/cmd/leaprc.protein.ff14SB
> ----- Source of
> /comptes/E117951H/amber/amber16/dat/leap/cmd/leaprc.protein.ff14SB done
> Log file: ./leap.log
> Loading parameters:
> /comptes/E117951H/amber/amber16/dat/leap/parm/parm10.dat
> Reading title:
> PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
> Loading parameters:
> /comptes/E117951H/amber/amber16/dat/leap/parm/frcmod.ff14SB
> Reading force field modification type file (frcmod)
> Reading title:
> ff14SB protein backbone and sidechain parameters
> Loading library: /comptes/E117951H/amber/amber16/dat/leap/lib/amino12.lib
> Loading library: /comptes/E117951H/amber/amber16/dat/leap/lib/aminoct12.lib
> Loading library: /comptes/E117951H/amber/amber16/dat/leap/lib/aminont12.lib
> > source leaprc.lipid17
> ----- Source: /comptes/E117951H/amber/amber16/dat/leap/cmd/leaprc.lipid17
> ----- Source of
> /comptes/E117951H/amber/amber16/dat/leap/cmd/leaprc.lipid17 done
> Log file: ./leap.log
> Loading parameters:
> /comptes/E117951H/amber/amber16/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: /comptes/E117951H/amber/amber16/dat/leap/lib/lipid17.lib
> com = lip_amber.pdb
> com = loadpdb lip_amber.pdb
> > com = lip_amber.pdb
> > com = loadpdb lip_amber.pdb
> Loading PDB file: ./lip_amber.pdb
> Warning: name change in pdb file residue 1 ;
> this residue is split into OL and PC.
> Warning: name change in pdb file residue 1 ;
> this residue is split into PC and OL.
> Warning: name change in pdb file residue 2 ;
> this residue is split into OL and PC.
> Warning: name change in pdb file residue 2 ;
> this residue is split into PC and OL.
> 4 residues had naming warnings.
> There are split residues;
> residue sequence numbers will not correspond to those in the pdb.
> total atoms in file: 564
> > savepdb com tleap.pdb
>
> Thx for your proposition Pr.Case,
> the lipid is still spliting from the head (PC) and the 2 lipid chain (OL).
> I even look in the leaprc.lipid17 file and lipid17.lib file. but it seem
> my file still have every atom search by the program.
> My question would be why is tleap still spliting my lipid in 3 residue.
>
> > On Wed, May 15, 2019, Maximilien BERNE wrote:
> >
> >>Loading PDB file: ./lip_amber.pdb
> >>Warning: name change in pdb file residue 1 ;
> >> this residue is split into OL and PC.
> >
> > Messages like this are expected.
> >
> >>Unknown residue: WAT number: 6 type: Terminal/beginning
> >
> > You need to "source leaprc.water.tip3p" (or choose another water model
> > here; see the beginning of Chap. 3 in the Reference manual).
> >
> > ...hope this helps....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
--
Stephan Schott Verdugo
Biochemist
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
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Received on Wed May 15 2019 - 11:00:02 PDT
