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

From: Maximilien BERNE <maximilien.berne.etu.univ-nantes.fr>
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
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 [ charmmlipid2amber.py -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-NuCP430rdz1DD2LkJxNM3BsKSjrw&m=FLo-bm3lLucv9-KTboTu4wQLl6oTzXGNHIg_9pUaTmM&s=cLXh23MuxaWzyKF4mxNwdl8YWEUoX7kOmj0ZCCDJOMo&e=
> ( i use AMBER16 )
> $AMBERHOME/bin/https://urldefense.proofpoint.com/v2/url?u=http-3A__charmmlipid2amber.py&d=DwIFAw&c=ZbgFmJjg4pdtrnL2HUJUDw&r=HwsFjSfOtLupDR-NuCP430rdz1DD2LkJxNM3BsKSjrw&m=FLo-bm3lLucv9-KTboTu4wQLl6oTzXGNHIg_9pUaTmM&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.
>>
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>>
>
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Received on Mon May 13 2019 - 08:30:03 PDT
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