> 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 |
---------------------------------------------------------
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Received on Fri May 11 2012 - 10:30:07 PDT
