Re: [AMBER] tleap split lipid when it shouldn't

From: Maximilien BERNE <>
Date: Mon, 13 May 2019 17:23:28 +0200 (CEST)

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

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 [ -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 <>
> Sent: Monday, May 13, 2019 10:37 AM
> To: AMBER Mailing List <>
> 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
> ( i use AMBER16 )
> -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 <>
>> Sent: Monday, May 13, 2019 8:42 AM
>> To:
>> 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.
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Received on Mon May 13 2019 - 08:30:03 PDT
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