Hi Maximilien,
The lipid-splitting issue seems to be coming from TER cards placed between
the residues of a single lipid molecule. For ordinary phospholipids, you
should have a TER card in the PDB file only after every three residues. I
see in the test.pdb file that you have one after every residue
(OL-TER-PC-TER-OL-TER...). Instead, it should be
OL-PC-OL-TER-OL-PC-OL-TER.... This can be fixed manually or with
charmmlipid2amber.py -- and probably other solutions are also available.
Best,
Sally
Sally Pias
Associate Professor of Chemistry
Faculty Adjunct, Department of Biology
New Mexico Tech
On Wed, May 15, 2019 at 4:18 AM Maximilien BERNE <
maximilien.berne.etu.univ-nantes.fr> wrote:
> Thx for your time ,
> i tryed your solution , but it doesn't change a thing
>
> Welcome to LEaP!
> (no leaprc in search path)
> > 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=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.
> Unknown residue: WAT number: 6 type: Terminal/beginning
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: WAT number: 7 type: Nonterminal
> [..] [[ due to WAT , but it isn't a probleme ]]
> > savepdb com test.pdb
> Writing pdb file: test.pdb
> > quit
>
> as you can see in test.pdb still split my lipid chain.
>
>
> > Try loading ff14SB before lipid17 in tleap, then load lip_amber.pdb:
> >
> > source leaprc.ff14SB
> > source leaprc.lipid17
> > com=loadpdb lip_amber.pdb
> >
> >
> >
> > -----Original Message-----
> > From: Maximilien BERNE <maximilien.berne.etu.univ-nantes.fr>
> > Sent: Monday, May 13, 2019 11:23 AM
> > To: AMBER Mailing List <amber.ambermd.org>
> > Subject: Re: [AMBER] tleap split lipid when it shouldn't
> >
> >
> > loading : lip_amber.pdb , won't change the output (chek-up the file :
> > lip_amber_tleap.pdb add in this mails) . Chain are still split.
> > The purpose of pdb4amber is to change our pdb file in to file that can be
> > ready by tleap, it wil delete water molecule (option --dry) and deleted
> > hydrogene ( option --nohyd ). so tleap will detecte our molecule and add
> > them ATOM folloing the force field chart of the residue/lipid.
> >
> > not using this step will cause to create some error when loading the pdb
> > file such as :
> > Creating new UNIT for residue: WAT sequence: 102 Created a new atom
> named:
> > O within residue: .R<WAT 102> Created a new atom named: H1 within
> residue:
> > .R<WAT 102> Created a new atom named: H2 within residue: .R<WAT 102>
> >
> > which bring those error when we want to create the prmtop file ad inpcrd
> > FATAL: Atom .R<WAT 102>.A<O 1> does not have a type.
> > FATAL: Atom .R<WAT 102>.A<H1 2> does not have a type.
> > FATAL: Atom .R<WAT 102>.A<H2 3> does not have a type.
> >
> >> I'm not familiar with pdb4amber (why is this step required?) but this
> >> is changing the format of your membrane PDB file such that it is not
> >> read correctly by tleap and the lipid force field.
> >>
> >> After charmmlipid2amber step [
> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__charmmlipid2amber.
> >>
> py&d=DwIFAw&c=ZbgFmJjg4pdtrnL2HUJUDw&r=HwsFjSfOtLupDR-NuCP430rdz1DD2LkJxNM3BsKSjrw&m=1g0z3By0QQHxFxNWsCY3Zt7jMJHbKzqSZaMFFvxObQE&s=3T2q0eOFYCtfwedpq9ZehNJZsxKdlXrJ4TZY8QTgvvA&e=
> >> -i step5_assembly.pdb -o lip_amber.pdb ] - you should load
> >> "lip_amber.pdb" directly into tleap, as this has the correct format as
> >> outlined in the lipid tutorial.
> >>
> >> It seems your reduce step just strips the hydrogens from the membrane
> >> - is there a reason for this step? Regardless, the membrane PDB you
> >> load finally into tleap should have lipid format matching
> >> "lip_amber.pdb".
> >>
> >> Best,
> >> Callum
> >>
> >>
> >> -----Original Message-----
> >> From: Maximilien BERNE <maximilien.berne.etu.univ-nantes.fr>
> >> Sent: Monday, May 13, 2019 10:37 AM
> >> To: AMBER Mailing List <amber.ambermd.org>
> >> Subject: Re: [AMBER] tleap split lipid when it shouldn't
> >>
> >> Hi,
> >> thanks for your time here's the step
> >> after creating my lipid with CHARMM-GUI i obtain this file (i recreate
> >> all the step with only 2 lipid) :
> >> -step5_assembly.pdb
> >>
> >> #then in terminal i use
> >> https://urldefense.proofpoint.com/v2/url?u=http-3A__charmmlipid2amber.
> >> py&d=DwIFAw&c=ZbgFmJjg4pdtrnL2HUJUDw&r=HwsFjSfOtLupDR-NuCP430rdz1DD2Lk
> >> JxNM3BsKSjrw&m=FLo-bm3lLucv9-KTboTu4wQLl6oTzXGNHIg_9pUaTmM&s=cLXh23Mux
> >> aWzyKF4mxNwdl8YWEUoX7kOmj0ZCCDJOMo&e=
> >> ( i use AMBER16 )
> >> $AMBERHOME/bin/https://urldefense.proofpoint.com/v2/url?u=http-3A__cha
> >> rmmlipid2amber.py&d=DwIFAw&c=ZbgFmJjg4pdtrnL2HUJUDw&r=HwsFjSfOtLupDR-N
> >> uCP430rdz1DD2LkJxNM3BsKSjrw&m=FLo-bm3lLucv9-KTboTu4wQLl6oTzXGNHIg_9pUa
> >> TmM&s=cLXh23MuxaWzyKF4mxNwdl8YWEUoX7kOmj0ZCCDJOMo&e=
> >> -i step5_assembly.pdb -o lip_amber.pdb
> >>
> >> #using pdb4amber to use it in tleap lip_amber.pdb =>
> >> lip_amber_reduce.pdb
> >>
> >> $AMBERHOME/bin/pdb4amber -i lip_amber.pdb --dry --nohyd --reduce
> >> --add-missing-atoms -o lip_amber_reduce.pdb -l
> >> BCL-Xl_mbrn_amber_reduce.log
> >>
> >> #then i load it in tleap
> >>
> >> tleap
> >> -I: Adding /comptes/E117951H/amber/amber16/dat/leap/prep to search path.
> >> -I: Adding /comptes/E117951H/amber/amber16/dat/leap/lib to search path.
> >> -I: Adding /comptes/E117951H/amber/amber16/dat/leap/parm to search path.
> >> -I: Adding /comptes/E117951H/amber/amber16/dat/leap/cmd to search path.
> >>
> >> Welcome to LEaP!
> >> (no leaprc in search path)
> >>> source leaprc.lipid17 #same happend using leaprc.lipid14
> >> ----- 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 = loadpdb lip_amber_reduce.pdb
> >> Loading PDB file: ./lip_amber_reduce.pdb
> >> total atoms in file: 108
> >> Leap added 168 missing atoms according to residue templates:
> >> 168 H / lone pairs
> >>> savepdb com lip_amber_reduce_tleap.pdb
> >> Writing pdb file: lip_amber_reduce_tleap.pdb
> >>> quit
> >>
> >> # and in this case i can see that my lip_amber_reduce_tleap.pdb in
> >> chimera has split my chain
> >>
> >> Thx for your time , hoping you know the probleme and help me solve it
> >>
> >> PS : i'm sorry that my mails send you a half-finish mailed due to an
> >> error.
> >>> Hi,
> >>>
> >>> Could you post the membrane PDB that you are loading into tleap? Or
> >>> at least a small part of it, like the first 2-3 lipids. Also, your
> >>> tleap command would be helpful.
> >>>
> >>> Best,
> >>> Callum
> >>>
> >>>
> >>> -----Original Message-----
> >>> From: Maximilien BERNE <maximilien.berne.etu.univ-nantes.fr>
> >>> Sent: Monday, May 13, 2019 8:42 AM
> >>> To: amber.ambermd.org
> >>> Subject: [AMBER] tleap split lipid when it shouldn't
> >>>
> >>> Dear AMBERs,
> >>>
> >>> i'm hoping you're having a nice day , and wish you could help someone
> >>> in need.
> >>>
> >>> So i try to make a MD on a protein with a lipid bilayer structure
> >>> (created with CHARMM-GUI). my lipid is only with DOPC
> >>>
> >>> using charmmlipid4amber, to create a file that will change my DOPC
> >>> into OL and PC.
> >>> I succed to create the prmtop file and inpcrd . but after simulation
> >>> i saw that my lipid are still split into three residues and that my
> >>> bilayer structure is slowly looking like a sphere when the head of
> >>> the lipid will just float around with water. I know that in force
> >>> field
> >>> lipid14 they split DOPC into those 3 residue.
> >>>
> >>> but i would like to know if there is a way to maintain those residue
> >>> together for my simulation.
> >>> i already tryed some things :
> >>> -scripting my files to recreate the bond between them, by deleting
> >>> TER when it's need it (but then tleap will split them again) -rename
> >>> my lipid in to OL , but then the ATOM (from PC) doesn't have a type
> >>> in tleap
> >>>
> >>> I join this with 2 images. First one from the lipid as it should be
> >>> (linked together) , and the second one when load into tleap (then
> >>> using savepdb to open it in chimera again) .
> >>>
> >>> I'm greatfull that you spend some times helping me.
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org
> >>> _
> >>> mailman_listinfo_amber&d=DwIFAw&c=ZbgFmJjg4pdtrnL2HUJUDw&r=HwsFjSfOtL
> >>> upDR-NuCP430rdz1DD2LkJxNM3BsKSjrw&m=FLo-bm3lLucv9-KTboTu4wQLl6oTzXGNH
> >>> Ig_9pUaTmM&s=TGKj8ddLg5Duv6rTXtsQiGzGGWdJnJRAM27QdObzs1g&e=
> >>>
> >>
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> >>
> >
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Received on Wed May 15 2019 - 15:30:03 PDT
