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

From: Maximilien BERNE <maximilien.berne.etu.univ-nantes.fr>
Date: Mon, 13 May 2019 16:37:09 +0200 (CEST)

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 charmmlipid2amber.py ( i use AMBER16 )
$AMBERHOME/bin/charmmlipid2amber.py -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
> http://lists.ambermd.org/mailman/listinfo/amber
>


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Received on Mon May 13 2019 - 08:00:02 PDT
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