Dear Maximilien,
I'm suspecting its a visualization issue, have you tried loading the prmtop and inpcrd files into VMD instead of a PDB file?
Then you can really see the actual bonds in your topology, otherwise molecular visualizing programs will guess about the atoms' connectivity according to some distance criteria.
Not seen some bonds in a PDB doesn't mean the atoms are not linked, it's just the bond length is larger than the cut-off to define them.
Best,
Matías
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[pasteur.uy/en/labs/biomolecular-simulations-laboratory/]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Maximilien BERNE" <maximilien.berne.etu.univ-nantes.fr>
Para: "david case" <david.case.rutgers.edu>, "AMBER Mailing List" <amber.ambermd.org>
Enviados: Miércoles, 15 de Mayo 2019 11:17:52
Asunto: Re: [AMBER] tleap split lipid when it shouldn't
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
>
>
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Received on Wed May 15 2019 - 10:30:02 PDT
