I followed the tutorial, used CHARMM-GUI to generate the protein embedded
in the lipid membrane, and add TER between the protein and the membrane.
The membrane is a mixture of POPC and POPS. Then I used
charmmlipid2amber.py to convert it into Amber format.
When I loaded the pdb file into xleap, it showed warnings as the tutorials
said, and then errors, as shown below.
Loading parameters: /opt/amber14/dat/leap/parm/lipid14.dat
Reading title:
AMBER Lipid14 Force Field, C. Dickson, B. Madej, A.Skjevik, K. Teigen, I.R.
Gould, R.C. Walker*
>>
>> # Load the Lipid14 master lib file.
>> # Note that other residues are stored in the lipid14_supp.lib file
and will be released at a later date.
>> loadoff lipid14.lib
Loading library: /opt/amber14/dat/leap/lib/lipid14.lib
Loading: CHL
Loading: LA
Loading: MY
Loading: OL
Loading: PA
Loading: PC
Loading: PE
>>
>
> source leaprc.ff14SB
----- Source: /opt/amber14/dat/leap/cmd/leaprc.ff14SB
----- Source of /opt/amber14/dat/leap/cmd/leaprc.ff14SB done
>> logFile leap.log
log started: Sat Jan 9 16:53:52 2016
......
> p = loadpdb prp-400.pdb
Loading PDB file: ./prp-400.pdb
Enter zPdbReadScan from call depth 0.
Warning: name change in pdb file residue 1 ;
this residue is split into PA 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 PA and PC.
Warning: name change in pdb file residue 2 ;
this residue is split into PC and OL.
Warning: name change in pdb file residue 3 ;
this residue is split into PA and PC.
Warning: name change in pdb file residue 3 ;
this residue is split into PC and OL.
Warning: name change in pdb file residue 4 ;
......
There are split residues;
residue sequence numbers will not correspond to those in the pdb.
Exit zPdbReadScan from call depth 0.
Matching PDB residue names to LEaP variables.
Mapped residue GLY, term: Terminal/beginning, seq. number: 0 to: NGLY.
(Residue 1: LYS, Nonterminal, was not found in name map.)
(Residue 2: ARG, Nonterminal, was not found in name map.)
(Residue 3: PRO, Nonterminal, was not found in name map.)
(Residue 4: LYS, Nonterminal, was not found in name map.)
(Residue 5: PRO, Nonterminal, was not found in name map.)
(Residue 6: GLY, Nonterminal, was not found in name map.)
(Residue 7: GLY, Nonterminal, was not found in name map.)
(Residue 8: TRP, Nonterminal, was not found in name map.)
(Residue 9: ASN, Nonterminal, was not found in name map.)
(Residue 10: THR, Nonterminal, was not found in name map.)
(Residue 11: GLY, Nonterminal, was not found in name map.)
(Residue 12: GLY, Nonterminal, was not found in name map.)
(Residue 13: SER, Nonterminal, was not found in name map.)
(Residue 14: ARG, Nonterminal, was not found in name map.)
(Residue 15: TYR, Nonterminal, was not found in name map.)
(Residue 16: PRO, Nonterminal, was not found in name map.)
(Residue 17: GLY, Nonterminal, was not found in name map.)
(Residue 18: GLN, Nonterminal, was not found in name map.)
(Residue 19: GLY, Nonterminal, was not found in name map.)
(Residue 20: SER, Nonterminal, was not found in name map.)
(Residue 21: PRO, Nonterminal, was not found in name map.)
(Residue 22: GLY, Nonterminal, was not found in name map.)
(Residue 23: GLY, Nonterminal, was not found in name map.)
(Residue 24: ASN, Nonterminal, was not found in name map.)
(Residue 25: ARG, Nonterminal, was not found in name map.)
(Residue 26: TYR, Nonterminal, was not found in name map.)
(Residue 27: PRO, Nonterminal, was not found in name map.)
(Residue 28: PRO, Nonterminal, was not found in name map.)
(Residue 29: GLN, Nonterminal, was not found in name map.)
(Residue 30: GLY, Nonterminal, was not found in name map.)
(Residue 31: GLY, Nonterminal, was not found in name map.)
(Residue 32: GLY, Nonterminal, was not found in name map.)
(Residue 33: GLY, Nonterminal, was not found in name map.)
(Residue 34: TRP, Nonterminal, was not found in name map.)
(Residue 35: GLY, Nonterminal, was not found in name map.)
(Residue 36: GLN, Nonterminal, was not found in name map.)
(Residue 37: PRO, Nonterminal, was not found in name map.)
(Residue 38: HSP, Nonterminal, was not found in name map.)
Unknown residue: HSP number: 38 type: Nonterminal
(Residue 39: GLY, Nonterminal, was not found in name map.
......
Starting new chain with K+
Starting new chain with K+
Starting new chain with K+
total atoms in file: 227864
Leap added 503 missing atoms according to residue templates:
7 Heavy
496 H / lone pairs
The file contained 13081 atoms not in residue templates
On Mon, Jan 11, 2016 at 12:34 AM, Jean-Marc <jmbillod.cib.csic.es> wrote:
> Hello,
> It is difficult to tell what is wrong without the pdb, could you please
> provide the one you're using? Did you try to load the pdb used in the
> tutorial into leap, does it work flawlessly?
> Best regards,
> Jean-Marc
>
>
>
> Sent from my iPhone
> > On 09 Jan 2016, at 23:40, Bin Wang <ben.wangbj.gmail.com> wrote:
> >
> > Dear Amber users,
> >
> > I followed the method in this website to install the AmberTools 15, and
> try
> > to use the lipdi14 force field with Amber 11
> > http://jswails.wikidot.com/installing-ambertools-14-and-older-amber
> >
> > Then I followed the Amber online tutorial 16 to get the membrane-protein
> > structure.
> > http://ambermd.org/tutorials/advanced/tutorial16/
> >
> > However, when I used xleap to load the pdb file of this membrane-protein
> > structure, the xleap showed a lot of errors such as these:
> >
> > Created a new atom named: C11 within residue: .R<PS 1969>
> > Created a new atom named: O12 within residue: .R<PS 1969>
> > One sided connection. Residue: default_name missing connect1 atom.
> > Creating new UNIT for residue: PS sequence: 1972
> > One sided connection. Residue: missing connect0 atom.
> > Created a new atom named: N31 within residue: .R<PS 1972>
> > Created a new atom named: HN1A within residue: .R<PS 1972>
> > Created a new atom named: HN1B within residue: .R<PS 1972>
> > Created a new atom named: HN1C within residue: .R<PS 1972>
> > Created a new atom named: C32 within residue: .R<PS 1972>
> > Created a new atom named: H2A within residue: .R<PS 1972>
> > Created a new atom named: C33 within residue: .R<PS 1972>
> > Created a new atom named: O35 within residue: .R<PS 1972>
> > Created a new atom named: O36 within residue: .R<PS 1972>
> >
> >
> > It seems that the xleap doesn't recognize the PS and PA lipid units in
> the
> > pdb file. I think I followed every step according to these tutorials, but
> > couldn't find out why it didn't work.
> >
> > Could anybody give me some suggestions? Thank you very much!
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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>
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Received on Mon Jan 11 2016 - 08:00:06 PST
