Re: [AMBER] lipid11 force filed question

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 11 May 2012 08:34:26 -0400

Please only send one email with the topic (you sent 4 within the span of a couple hours). The lipid11 force field developer is typically fairly responsive on this list and you should receive an answer within a reasonable period of time.

Also remember that oftentimes the responders are in a different time zone than you are -- at the time of your first email they were very likely asleep for the night and have probably still not woken.

All the best,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On May 11, 2012, at 6:19 AM, Tales Yuan <yukitenkou.gmail.com> wrote:
> 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 - 06:00:04 PDT