Le 03/03/2011 22:02, Baptiste Legrand a écrit :
> Le 03/03/2011 19:54, Daniel Roe a écrit :
>> Hi,
>>
>> On Thu, Mar 3, 2011 at 12:21 PM, Baptiste
>> Legrand<bap.legrand.gmail.com> wrote:
>>> I have first tried to trajin all my rst but it seems that only the
>>> first
>>> file is taken in account:
>> How do you know only the first file is taken into account (are there
>> error messages etc)?
>>
>>> So in a second stage, I have concatenated with the cat command and then
>>> launch the my traj script:
>> You can't concatentate restart files - by design they contain only one
>> set of coordinates (and optionally velocities). Only the first set
>> will be read.
>>
>>> Checking coordinates: all.rst
>>> readAmberRestart(): topology/coordinates file are inconsist with
>>> NATOMS = 1138 (1248)
>> This indicates that the number of atoms in your topology does not
>> match the number of atoms in the restart file, I suspect as a result
>> of the 'STRIP :CL3'. You would need to generate a new topology file
>> without :CL3 in order to process files stripped of :CL3.
>>
>> -Dan
>>
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> Thanks, indeed I used the bad topology files. This new script works
> fine. I have just a problem with the "average average.rst rest" which
> generates an empty rst file...
>
> for x in `seq 1 20`
> do
> cat > trajin <<EOF
> trajin C70_$x.rst
> STRIP :CL3
> trajout C70s_$x.rst
> EOF
> ptraj ../prep/C70_$x.prmtop < trajin
> done
> cat > trajin <<EOF
> trajin C70s_1.rst
> trajin C70s_2.rst
> ...
> rms first mass out all.fit .N1,C9,C11,N2,C12,C17,C20,N3,C21,C29,N4
> image center familiar
> average average.pdb pdb
> average average.rst rest
> EOF
> ptraj C70.prmtop < trajin
> #sander -O -i min.in -o C70.out -c average.rst -p C70.prmtop -r
> C70mean.rst
Then, starting from the average.pdb file, I have used my initial prepin
file (without solvent box) to generate inpcrd and prmtop (check with
VMD) to minimize the average structure.
sander -O -i min.in -c average.inpcrd -p average.prmtop -r C70_mean.rst
However, nothing happen when I launch the minimization and the out file
is empty with just these lines:
--------------------------------------------------
Amber 10 SANDER 2008
--------------------------------------------------
The minimization script in this case might be wrong, I have used this
one from the tutorial1:
polyA-polyT 10-mer: initial minimization prior to MD
&cntrl
imin = 1,
maxcyc = 500,
ncyc = 250,
ntb = 0,
igb = 0,
cut = 12
/
Thanks,
Baptiste
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Received on Fri Mar 04 2011 - 02:30:02 PST
