Thank you very much.
The mailing system told me that my email delivered failed. So I'm not sure
that the email has sent out or not. I'm sorry for the duplicate topic.
Best regards,
2012/5/11 Jason Swails <jason.swails.gmail.com>
> 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.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri May 11 2012 - 06:00:06 PDT
