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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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Mon Jan 11 2016 - 08:30:05 PST
