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
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Sep 02 2014 - 06:30:03 PDT
