Dear Amber Users,
I tried to leap DPPE lipid by using lipid11 force field in AmberTools12,
but there is a problem. It splits a DPPE molecule into three parts.
I used Charmm-GUI to get a DPPE pdb file. Then I used charmmlipid2amber.x (
the new version in mailing list ) to convert it. It seems correct.
*ATOM 33 C12 PA 1 ... MEMB*
*...*
*ATOM 121 H16T PA 1 ... MEMB*
*ATOM 1 N31 PE 1 ... MEMB*
*...*
*ATOM 32 O12 PE 1 ... MEMB*
*ATOM 24 C12 PA 1 ... MEMB*
*...*
*ATOM 78 H16T PA 1 ... MEMB*
*TER *
*
*
After checking the pdb file, I used tleap to get the prmtop, inpcrd and new
pdb files.
*source leaprc.lipid11*
*dppe = loadpdb dppe.pdb*
*savepdb dppe_new.pdb*
*saveamberparm dppe.prmtop dppe.inpcrd*
Then I checked dppe_new.pdb, it like this:
*ATOM 1 C116 PA 1 ...*
*...*
*ATOM 46 H2S PA 1 ...*
*TER*
*ATOM 47 C11 PE 2 ...*
*...*
*ATOM 75 O22 PE 2 ...*
*TER*
*ATOM 76 C116 PA 3 ...*
*...*
*ATOM 121 H2S PA 3 ...*
*TER*
A dppe molecule was splited to three residues. So how can I get the correct
results without the redundant "TER" ?
The informations in leap.log is listed below.
*> dppe = loadpdb dppe.pdb*
*Loading PDB file: ./dppe.pdb*
*Enter zPdbReadScan from call depth 0.*
*Warning: name change in pdb file residue 1 ;*
* this residue is split into PA and PE.*
*Warning: name change in pdb file residue 1 ;*
* this residue is split into PE and PA.*
*2 residues had naming warnings.*
* 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.*
*(Residue 0: PA, Terminal/beginning, was not found in name map.)*
*(Residue 1: PE, Nonterminal, was not found in name map.)*
*(Residue 2: PA, Terminal/last, was not found in name map.)*
*Joining PA - PE*
*Joining PE - PA*
* total atoms in file: 121*
*> savepdb dppe dppe_new.pdb*
*Writing pdb file: dppe_new.pdb*
*> saveamberparm dppe dppe.prmtop dppe.inpcrd*
*Checking Unit.*
*Building topology.*
*Building atom parameters.*
*Building bond parameters.*
*Building angle parameters.*
*Building proper torsion parameters.*
*Building improper torsion parameters.*
* total 2 improper torsions applied*
*Building H-Bond parameters.*
*Not Marking per-residue atom chain types.*
*Marking per-residue atom chain types.*
* (Residues lacking connect0/connect1 - *
* these don't have chain types marked:*
*
*
* res total affected*
*
*
* PA 2*
* PE 1*
* )*
* (no restraints)*
*
*
Thank you very much.
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Received on Fri May 11 2012 - 01:00:04 PDT
