The renaming is normal since each residue should have a unique number
however you have several errors:
In the protein part you are using HSP which is not recognized by
AMBER, one should use HIE/HID/HIP.
Since residue PS is from LIPID11, you want to make sure to load
lipid14_supp.lib or lipid11.lib (loadoff PATH/lipid14_supp.lib).
Something else is strange with the protein part, do you have a "TER"
between each amino acid?
Jean-Marc
Quoting Bin Wang <ben.wangbj.gmail.com>:
> 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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>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Mon Jan 11 2016 - 09:00:04 PST
