Hi, Thomas
I found the reason.
Actually, I misunderstood your tutorial and used same crd file for
transformation procedure,
but now I use different crd files for each process, and it works fine.
However, I have another problem.
Previously, it was TI calculation to transform from HIP to HIE, and it
works fine.
Additionally, I also tried TI calculation to transform from CYS to
CYM.(deprotonated CYS)
However, this gives an error below.
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 696
| Atom division among processors:
| 0 2111
Softcore Mask .15; matches 1 atoms
this run corresponds to V0, its softcore atoms interact fully for
lambda=0
this process: 2111 atoms, partner process: 2110 atoms
Checking for mismatched coordinates.
WARNING: Local coordinate 34 differs from partner coordinate
34 !
SANDER BOMB in subroutine sc_check_and_adjust
Atom coordinate disagreement
Check input files.
I know that this error occurs when the coordinates of two crd files are
different significantly,
but I checked several times and am quite sure that there is no
difference between two crd files except the coordinate of disappearing
atom.
What I found very strange is it did work for histidine case but not for
cysteine case.
(I did exactly same for both cases.)
Do you have any idea about this problem?
Cheers,
Wook
On 07/19/2012 05:36 PM, steinbrt.rci.rutgers.edu wrote:
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Jul 21 2012 - 06:30:02 PDT
