Hi,
I am trying to simulate a transporter protein embedded in POPC membrane. I have used CHARMM-GUI to build the assembly. I used charmmlipid2amber.x (
http://ambermd.org/tutorials/advanced/tutorial16/An_Amber_Lipid_Force_Field_Tutorial.html) to convert CHARMM format to Amber. Following which, I loaded lipid11 and FF99SB force fields in leap, and loaded the assembly to the leap. However I ended up with having error termination regarding atom nomenclature in the complex. The protein alone went well with the leap to generate top file.
Any suggestion and/or help is appreciated.
thanks,
Dipankar Roy
Excerpt from leap.log
ated a new atom named: HG1 within residue: .R<SER 420>
Joining SER - ILE
Created a new atom named: HN within residue: .R<ILE 421>
Created a new atom named: HG11 within residue: .R<ILE 421>
Created a new atom named: CD within residue: .R<ILE 421>
Created a new atom named: HD1 within residue: .R<ILE 421>
Created a new atom named: HD2 within residue: .R<ILE 421>
Created a new atom named: HD3 within residue: .R<ILE 421>
Added missing heavy atom: .R<ILE 421>.A<CD1 14>
Joining ILE - ILE
Created a new atom named: HN within residue: .R<ILE 422>
Created a new atom named: HG11 within residue: .R<ILE 422>
Created a new atom named: CD within residue: .R<ILE 422>
Created a new atom named: HD1 within residue: .R<ILE 422>
Created a new atom named: HD2 within residue: .R<ILE 422>
Created a new atom named: HD3 within residue: .R<ILE 422>
Added missing heavy atom: .R<ILE 422>.A<CD1 14>
Joining ILE - THR
Created a new atom named: HN within residue: .R<THR 423>
Joining THR - GLN
Created a new atom named: HN within residue: .R<GLN 424>
Created a new atom named: HB1 within residue: .R<GLN 424>
Created a new atom named: HG1 within residue: .R<GLN 424>
Created a new atom named: OT1 within residue: .R<GLN 424>
Created a new atom named: OT2 within residue: .R<GLN 424>
Added missing heavy atom: .R<GLN 424>.A<O 17>
Joining GLN - PA
ERROR: Comparing atoms
.R<PA 425>.A<C13 41>,
.R<GLN 424>.A<C 16>,
.R<PA 425>.A<H2R 45>, and
.R<PA 425>.A<H2S 46>
to atoms
.R<PA 425>.A<C13 41>,
.R<PC 1>.A<C11 5>,
.R<PA 425>.A<H2R 45>, and
.R<GLN 424>.A<C 16>
This error may be due to faulty Connection atoms.
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Received on Tue May 07 2013 - 10:00:04 PDT
