Yes, 5365. What happened will be discovered. Up to the stage on

amber_score_everything, all was perfectly OK. Minimization and heating was also

OK. As to MD, the situation could not be clarified so far. 

In view of your comments below, I carried out a check with proven MD. I went to

Amber tutorial B3, took equil1.mdcrd.gz, decompressed, took the related prmtop,

and fed the two files to Chimera, last Daily Building. After all 5000 steps had

been acquired, saved pdb, all frames. Quit MD Movie. Try to open this pdb.

Well, with my modest desktop, Debian Linux i386, 1GB ram, this pdb could not be

opened: rapidly the memory was exhausted and to get control of the computer I

had to kill gnome. With vmd, this pdb developed rapidly with all 5000 frames.

Exactly as with the pdb from MD with my protein. This does not mean that my MDs

are OK. I'll look for what may be wrong there.

Thanks

francesco

--- Eric Pettersen <pett@cgl.ucsf.edu> wrote:

5365 atoms?  Given average atom counts in protonated protein residues  

that means your ligand came in close contact with ~340 residues over  

the course of the trajectory -- so it's wandering all over the  

place.  I can see why you want to use cluster analysis.  Oh well, I  

guess we're stuck until I have time to coordinate with Conrad and  

integrate his clustering code with MD Movie.

--Eric

On Jan 10, 2008, at 6:38 AM, Francesco Pietra wrote:

Eric: I followed previous route from combined mdcrd from ptraj.

Removed remaining water.

select ligand z<2.5

as Chimera command; (this was the minimum, selecting 244 atoms, 118  

of which

for the ligand; with z<2.0 the ligand only is selected)

On playing the pdb (saved for selected atoms only) (with LOOP  

deselected) the

atom selection increased, reaching 5365 atoms at the last (549)  

frame. In

another run, with z<4.0 the course of atom selection was similar,  

reaching 5993

atoms at frame 549.

This huge number of atoms proved problematic for opening pdb. For  

the z<2.5

case I left the computer on for 4h and half, with python occupying  

98% of the

available MEM (nearly 1GB). I had to kill gnome to recover command.

May be with much more MEM it will work, though I can't check that now.

I did not try to combine the trajectories with Chimera as I have no  

indication

that those from ptraj are faulty. The pdb files for both z<2.5 and  

z<4.0 open

in vmd.

francesco

--- Eric Pettersen <pett@cgl.ucsf.edu> wrote:

On Jan 9, 2008, at 3:32 PM, Francesco Pietra wrote:

In the "Define script.." I defined "select ligand z<10", then OK

and a BUG

window was presented. Attached is the reply log (bug). I tried with

z<4 with

the same result (actually, I don't remember if attached bug file

refers to z<10

or z<4).

In the script-definition dialog you need to have "Interpret script

as" set to "Chimera commands".  You had it set to "Python".

Still found difficulties in loading more than one mdcrd, though

this should be

my fault. I was not sure if the list of mdcrd is to be given at

beginning or if

the other mdcrd files after the first one are to be given

subsequently from the

menu. I tried with the "list" option but only the first mdcrd was

opened.

When you run MD Movie and the dialog comes up where you specify the

prmtop/trajectory files, you can use the "Add..." button to add as

many trajectory files as needed.  I think this means you "give it at

the beginning" rather than "subsequently from the menu" in your

terminology.

You can also just list the files in a "metafile" for the command

line.  For instance, this file works for me:

amber

leap.top

md01.crd

md02.crd

md03.crd

md04.crd

md05.crd

md06.crd

Note that there _still_ seems to be something funky with Amber

compressed trajectories, so don't use them for now but I should have

things fixed in a day or so with that.

--Eric

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