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

From: Maximilien BERNE <maximilien.berne.etu.univ-nantes.fr>
Date: Wed, 15 May 2019 12:18:29 +0200 (CEST)

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 - 03:30:03 PDT
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