Hi,
the procedure looks right, but make sure that each of your individual
prmtop files can be used to run a normal amber simulation first. What you
see is no TI error, but looks like the prmtop and restrt file do not
match.
setbox is in the Ambertools manual and defines a system as having a
periodic box, which pdbs dont have automatically.
Thomas
On Thu, July 19, 2012 11:19 am, Wook Lee wrote:
> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Thu Jul 19 2012 - 09:00:03 PDT
