Hi Tales,
> 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.
This is correct. As in the format should be 1Tail1, 1Head, 1Tail2, TER,
2Tail1, 2Head, 2Tail2, TER, ...
> 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.
Yeap so this all looks good at this point.
> *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" ?
This looks like a bug in the Leap code itself. Ben can you take a look at
this and see if you reproduce the behavior please and if so file a bug
report for Leap.
What happens if you use ptraj to make your pdb file instead of leap?
I.e.
trajin dppe.inpcrd
trajout dppe_new.pdb pdb
Does this still put the TER cards in between the residues within the three
residues making up a lipid unit?
For the moment if that doesn't work the solution, I am afraid, is to go
through and manually remove all the excess TER cards. It shouldn't be too
hard to script though, you basically need a loop that removes the first 2
out of every three TER cards in the file. Then you should be able to use
this again in Leap - I assume so that you can insert a protein in the lipid
file yes? - Otherwise why are you reading the pdb file back in?
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Fri May 11 2012 - 08:30:04 PDT
