Hi,
CPPTRAJ currently won't recognize these trajectories. A fix is in
progress. In the meantime, you may be able to temporarily get around
this by changing the first 4 characters of your trajectory file from
'RXSG' to 'REMD' and using the remdtraj/remdtrajtemp keywords in place
of rxsgldtraj/rxsgldid, as I believe all of the trajectory processing
functionality is otherwise the same.
Alternatively, you could use cpptraj or parmed to convert your
CHAMBER topology to an Amber one suitable for trajectory processing
with ptraj. For cpptraj this is just:
parm chamber22gro.prmtop
parmwrite out myparm.parm7 nochamber
Hope this helps, and thanks for the report.
-Dan
On Tue, Sep 2, 2014 at 7:40 AM, wliu <wliu.itcs.ecnu.edu.cn> wrote:
> Hi,Jason
>
> I try CPPTRAJ just now, but it says that:
>
> CPPTRAJ: Trajectory Analysis. V14.00
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
> Reading '../step5/chamber22gro.prmtop' as Amber Topology
> CHAMBER topology: 1: CHARMM 31 * CHARMM22STAR CHARMM22STAR
> CHARMM22STAR CHARMM22STAR CHARMM
> INPUT: Reading Input from STDIN
> [trajin ../step5/crd/rxsg25.mdcrd.001 rxsgldtraj rxsgldid 1]
> Error: Could not determine trajectory ../step5/crd/rxsg25.mdcrd.001
> format.
> Error: Could not set up input trajectory
> '../step5/crd/rxsg25.mdcrd.001'.
> 1 errors encountered reading input.
> TIME: Total execution time: 0.0883 seconds.
>
> Need your help!
>
> Wei Liu
>
> On 2014-09-02 21:27, Jason Swails wrote:
>> On Tue, Sep 2, 2014 at 9:05 AM, wliu <wliu.itcs.ecnu.edu.cn> wrote:
>>
>>> Hi all,
>>>
>>> Recently I use CHAMBER program transformed CHARMM parameter file
>>> to
>>> AMBER prmtop file and run a replica exchanging self-guided (RXSG)
>>> MD. I
>>> met the problem when I use ptraj to extract the RXSG MD trajectory.
>>> The
>>> error information was shown as follows:
>>>
>>> WARNING in scanDouble: ...scanning chrg
>>>
>>> Residue labels:
>>>
>>> TYR TYR ASP PRO GLU THR GLY THR TRP TYR
>>> SOD SOD WAT WAT WAT WAT WAT WAT WAT WAT
>>> WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
>>> ...
>>> WAT WAT WAT WAT WAT
>>>
>>> There were errors upon reading parm file!!!
>>>
>>> PTRAJ: Processing input from "STDIN" ...
>>>
>>> PTRAJ: trajin ../step5/crd/rxsg25.mdcrd.001 rxsgldtraj rxsgldid 1
>>> Checking coordinates: ../step5/crd/rxsg25.mdcrd.001
>>>
>>> It seems that ptraj can't recognize my parm file. So I also
>>> update
>>> Amber12 to do some patching, but still have the same problem. I know
>>> that the parm file from CHARMM force field using CHAMBER may have
>>> some
>>> differences from AMBER parm on format like %FLAG CHARGEļ¼
>>> charmm to amber parm file:
>>> %FORMAT(3e24.16)
>>> -0.5466849549786422E+01 0.6013534504765064E+01
>>> 0.6013534504765064E+01
>>> 0.6013534504765064E+01 0.3826794684850495E+01
>>> 0.1822283183262141E+01
>>> -0.3280109729871853E+01 0.1640054864935927E+01
>>> 0.1640054864935927E+01
>>> but amber parm file:
>>> %FLAG CHARGE
>>> %FORMAT(5E16.8)
>>> 3.36930327E+00 3.45859254E+00 3.45859254E+00 3.45859254E+00
>>> 1.03320441E+00
>>> 1.42498386E+00 4.73050908E+00 4.97468790E-01 4.97468790E-01
>>> -1.22344522E+01
>>> and charmm to amber file seems to have no %FLAG BOX_DIMENSIONS
>>> information in parm file. But I have already run the simulation
>>> using
>>> this parm file successfully. So I think this parm file is ok.
>>> I have no idea about this error. I wonder how to solve the
>>> problem
>>> and why ptraj can't read my parm file?
>>>
>>
>> Use cpptraj instead. cpptraj understands chamber topology files.
>>
>> HTH,
>> Jason
>>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Sep 02 2014 - 07:00:04 PDT
