Hi, Thomas
Thank you for your reply.
I tried your suggestion, but I got an error below.
FATAL: NATOM mismatch in coord and topology files
I generated two prmtop files as written in your tutorial.
What I did are as follows,
First, I generated pdb file using tleap
source leaprc.ff99SB
a = sequence{ACE HIP NME}
solvateoct a TIP3PBOX 10
savepdb a start.pdb
Then, I modified start.pdb.
I deleted one hydrogen atom and rename and changed the residue name from
HIP to HIE,
and saved it as end.pdb
Then I generated two prmtop and two rst file using tleap.
source leaprc.ff99SB
prot = loadpdb start.pdb
setbox prot vdw
saveamberparm prot a.prmtop a.rst
prot = loadpdb end.pdb
setbox prot vdw
saveamberparm prot b.prmtop b.rst
Is there anything wrong in this procedure?
Also, what does the setbox command do?
I searched the manual, but I can't find anything related to setbox in
amber11 manual.
Cheers,
Wook
On 07/19/2012 04:19 PM, steinbrt.rci.rutgers.edu wrote:
> Hi,
>
>> However, I got a problem in step 2 where the atom is supposed to
>> disappear.
> The problem is here:
>
>> &cntrl
>> imin=0, ntb=2, ntx=5, irest=1,
>> cut=8.0, ntp=1,
>> temp0=310.0, ntf=1, ntc=2,
>> ntt=3, gamma_ln=5.0,
>> nstlim=500000, dt=0.002, iwrap=1,
>> ntpr=500, ntave=500,
>> icfe=1, clambda=0.04691,
>> /
> you need to set ifsc=1 on both processes, otherwise they will not know how
> to communicate with each other and your softcore side waits forever for a
> reply from the other process.
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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>
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Received on Thu Jul 19 2012 - 08:30:02 PDT
