hi all,
I now have new problems. The MD runs finished fine. I modified the
ions08.lib file as suggested by Dr. Case. However when I try to perform a
MMPBSA calculation on the generated trajectories, it never went
through.(AmberTools 1.5 updated with all the patch files) I see all these
huge clashes in the _MMPBSA_***_gb.mdout files, such as:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 3.7213E+16 7.8320E+16 5.1146E+18 HA 3273
BOND = 23438545.8760 ANGLE = 368673.1288 DIHED =
14366.0233
VDWAALS = ************* EEL = 65872.2873 EGB =
-76922.3045
1-4 VDW = ************* 1-4 EEL = -15976.3752 RESTRAINT =
0.0000
ESURF = 116.6306
TDC 20-> 110 0.000 ********* -35.821 30.160 -47.364
TDC 21-> 3 0.000 -0.006 7.620 -7.734 0.000
TDC 21-> 20 0.000 52439.487 41.109 -29.840 -119.690
TDC 21-> 21 0.000 ********* 25.121 -55.899 515.825
However the md output files looks fine. And I did generate receptor, ligand
etc param files with the modified library. I'm not sure Mg is the cause
here though I really can't think of anything else. I did the same
calculation without the mg but with Na as counterions only. And everything
worked fine.
So how can I fix this? Thanks a lot.
Victor
On Tue, Nov 1, 2011 at 1:09 PM, Victor Ma <victordsmagift.gmail.com> wrote:
> Plan A worked fine. Thanks a lot, Dr. Case.
>
> Victor
>
>
> On Tue, Nov 1, 2011 at 10:51 AM, David A Case <case.biomaps.rutgers.edu>wrote:
>
>> On Tue, Nov 01, 2011, Victor Ma wrote:
>> >
>> > I'm running AMBER on a cluster and I have no authority to change the
>> > $AMBERHOME/dat/leap/lib files. So is there an easy way to do it locally?
>>
>> Copy everything in $AMBERHOME/dat/leap to some local directory you have
>> control over. Then, when you load ions8.lib, point specifically to the
>> local
>> copy you have changed.
>>
>> Or: copy everything under $AMBERHOME to your local directory, set your
>> AMBERHOME variable to point to the new location, and recompile all the
>> programs. This has the advantage that Amber is now under *your* control,
>> but
>> you may have a learning curve as well.
>>
>> ....dac
>>
>>
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>>
>
>
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Received on Tue Nov 08 2011 - 09:30:06 PST
