On May 11, 2012, at 8:43 AM, Tales Yuan <yukitenkou.gmail.com> wrote:
> 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.
Ah, that happens from time to time. At least you know your mail has been received ;)
>
> 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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>>
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Received on Fri May 11 2012 - 06:00:07 PDT
