Thanks very much for your reply and your hard work.
I have checked it in VMD by reading prmtop/inpcrd. The head group bonds to
tail correctly.
Best regards
2012/5/12 Ross Walker <ross.rosswalker.co.uk>
> > Thanks Walker. I use Amber11 + AmberTools12 now. I set $AMBERHOME to
> > amber12 directory as the manual said, and set the amber12/bin before
> > amber11/bin in PATH.(Page 23)
> >
> > *echo $AMBERHOME*
> > */home/user/amber12*
> > *echo $PATH*
> > */home/user/amber12/bin:/home/user/amber11/bin:/usr/local/cuda/bin:/...
> > ....*
> > *which tleap*
> > *~/amber12/bin/tleap*
> >
> > I tried ptraj and ambpdb to convert pdb from inpcrd/prmtop.
> >
> > *ptraj dppe.prmtop ptraj.in* (dppe_new1.pdb)
> > *ampbpdb -p dppe.prmtop < dppe.inpcrd > dppe_new2.pdb*
> >
> > In new1 pdb, there is NO TER card in pdbfile, either lipids or water. (
>
> Water is to be expected, none of the AMBER tools have included TER cards
> between water residues and Leap handles this explicitly.
>
> There should however be TER cards BETWEEN each lipid molecule, where each
> lipid molecule is made up of THREE residues. So as I say it should be as
> you
> see for new2.pdb made with ambpdb:
>
> > I
> > tried a pdb including TIP3P water )
> > In new2 pdb, the TER cards seems good.
> > *PA 1*
> > *PE 2*
> > *PA 3*
> > *TER*
> > *PA 4*
> > *PE 5*
> > *PA 6*
> > *TER*
> > *...*
>
> Perfect... It is crazy that the 30 year old code is the only one that seems
> to be doing things properly. Sigh...
>
> We'll take a look at it and see if we can figure out what is going on.
>
> 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 |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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Received on Fri May 11 2012 - 11:00:03 PDT
