Re: [AMBER] meeting a problem when using ptraj to extract the replica exchanging self-guided MD trajectory

From: wliu <wliu.itcs.ecnu.edu.cn>
Date: Tue, 02 Sep 2014 22:08:44 +0800

Hi, Dan

   Thank you for your reply and solutions! I will try your suggestions!

Wei Liu

On 2014-09-02 21:59, Daniel Roe wrote:
> 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 CHARGE：
>>>> 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 - 07:30:02 PDT