Dr. Walker,
I followed the instruction from this website to install AmberTools 15, and
try to use the lipid14 force field with Amber 11.
http://jswails.wikidot.com/installing-ambertools-14-and-older-amber
I don't know what I did wrong, but so far it still not working.
Bin
On Mon, Jan 11, 2016 at 11:18 AM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Bin,
>
> Are you really using AMBER 11 here? I don't think we've ever tested Lipid
> 14 with AMBER 11 and the conversion scripts etc were not available until
> AMBER 14 and have been updated since then. I would suggest downloading
> AmberTools 15 from the amber website (http://ambermd.org/) and using the
> tools from there. Once you have your prmtop and inpcrd file it should be
> possible to run that with pmemd from Amber 11 if you do not have a newer
> version.
>
> All the best
> Ross
>
> > On Jan 11, 2016, at 07:45, Bin Wang <ben.wangbj.gmail.com> wrote:
> >
> > 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!
> >>> _______________________________________________
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> >>
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Received on Mon Jan 11 2016 - 08:30:07 PST
