On Tue, Apr 21, 2015 at 12:16 PM, Vaibhav Dixit <vaibhavadixit.gmail.com>
wrote:
> Hi all,
> Thanks everybody for your vital inputs and explanation on the possible bug.
> The detailed output from the tleap including saveambeparm command is given
> at the end here (sorry for not including the whole thing earlier).
> I will check with our system admin for the updates.
>
Your leap output shows that everything completed successfully. The
problem is almost certainly the bug I mentioned in my previous email.
You can use the command
$AMBERHOME/update_amber --version
to print out which updates have been applied. I strongly suspect that the
answer is none. In which case, the admin will need to reconfigure and
recompile Amber on the machine.
Alternatively, you can download AmberTools 14 yourself and install it. But
until Amber is updated, it might be hard to work around this bug. You
could try to add another saveAmberParm command in order to *force* buffer
flushing (I'm not sure if this will work or not). So something like this:
source leaprc.ff14SB
source leaprc.gaff
CYP = loadmol2 CYS_HS.mol2
set CYP head CYP.1.N
set CYP tail CYP.1.C
desc CYP
HEM = loadmol2 HEM_pentacoordinateHS.mol2
loadamberparams HEM_HS.frcmod
loadamberparams frcmod.ionsjc_tip3p
P450 = loadpdb 1W0E_P450_leap.pdb
bond P450.419.SG <
http://p450.419.sg/> P450.477.FE
solvateoct P450 TIP3PBOX 12
charge P450
addions P450 Cl- 0
saveAmberParm
P450 P450_1W0E_1.prmtop P450_1W0E_1.inpcrd
saveAmberParm
P450
junk.prmtop junk.inpcrd
Hopefully writing the junk.* files will flush the buffers for
P450_1W0E_1.inpcrd. If not, you will have to wait for an update from the
sysadmin.
> Just wondering is there a way to specify increased memory to sander and how
> much in this case may be required (15049 atoms after adding waters), if
> that's one of the issue beside the updates.
>
It's not. Your input file is truncated, so it's missing information that
sander and pmemd need for the simulation. The only way you can "fix" this
is by providing an inpcrd file that is not truncated (memory amounts in
sander are entirely unrelated to this).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Apr 21 2015 - 11:00:03 PDT
