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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Received on Tue Sep 02 2014 - 07:00:03 PDT
