Hi Edo,
> Following CS advice, I changed nbt from 0 to 1 but I'm still
> having problem
> More in details I'm trying to minimize a system in water and
> then using
> this for PBSA calculations:
>
> I attached all scripts I'm using
>
> I'm doing the following:
>
> - with two separate Leaps I add ions (leap_1) and waterbox (leap_2)
> (t_leap.run)
Looking at your leap scripts:
source leaprc.gaff
loadamberparams ../../Dati_LEAP/parm_copZ.dat
loadAmberPrep ../../Dati_LEAP/CU.prep
loadAmberPrep ../../Dati_LEAP/CYG.prep
MNK = loadPdb neweditin.pdb
bond MNK.148.CU MNK.12.SG
bond MNK.148.CU MNK.87.SG
bond MNK.148.CU MNK.90.SG
addions MNK Na+ 6
saveAmberParm MNK prm_1.top prm_1.crd
savepdb MNK prm_1.pdb
quit
I see no evidence of you adding a solvent box here so what you have is a
system that is in gas phase with some ions around it. There will be no box
information in the crd file since you didn't add any solvent or specify box
parameters.
The water minimization input file has:
REM
&cntrl
imin=1,
maxcyc=1000, ncyc=400,
scee=1.2,
ntpr=100,
ntwx=100,
cut=15.0,
ntb=0,
ntr=1,
/
Hold the Protein fixed
500.0
RES 1 148
END
END
So here you have ntb=0 which implies gas phase which is consistent with your
input files. Hence this part of the calculation should probably run okay and
at the end you get a restart file for a gas phase system.
Then when you move to min prot:
REM
&cntrl
imin=1,
maxcyc=1000, ncyc=400,
scee=1.2,
ntpr=100,
ntwx=100,
cut=15.0,
ntb=1,
ntr=1,
/
Hold the Protein fixed
500.0
RES 155 2226
END
END
You set ntb=1 which implies a periodic system. Thus the code then expects
box information to be present at the end of the restart file which obviously
isn't there because the previous run was a gas phase simulation. Hence it
hangs. The code probably should stop with an error here but this is fairly
difficult to trap since it is streaming in the inpcrd file and just waiting
for the extra box information numbers which never appear. Note here I assume
you are trying to hold the water fixed although the comment reads hold the
protein fixed. Note from your leap input files I can't see where residues
155 to 2226 actually made it into the prmtop file so you may also have
problems here with the restraint code looking for residues that don't exist.
You should also note that when running explicit solvent simulations with PME
(the default) you do not need to use such a large cut off as 15.0. Something
around 8.0 or 9.0 is probably good.
Good luck,
Ross
/\
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|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
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Received on Mon Sep 24 2007 - 17:45:31 PDT
