AMBER Archive (2008)

Subject: Re: AMBER: PTRAJ - Segmentation Fault

From: Jianyin Shao (jyshao2004_at_gmail.com)
Date: Wed Jun 11 2008 - 11:01:07 CDT

On 6/10/08, dpandit_at_brandeis.edu <dpandit_at_brandeis.edu> wrote:
>
> Hi All:
> I wanted to perform analysis on output trajectory file using ptraj but I
> get error of segmentation fault. Below is the error and input file of ptraj.
>
>
> Thank you for the help!
> Deepa
>
> Error:
>
> [dpandit_at_hpc hGH]$ /share/apps/amber9/exe/ptraj hgh_sol_apr7.prmtop <
> merge_mdcrd_reimaged.ptraj > merge_mdcrd_reimaged.out
> Residue labels:
>
> Checking coordinates: eq_pro_hGH.mdcrd
> Segmentation fault
> [dpandit_at_hpc hGH]$
>
>
> Input File
>
> trajin eq_pro_hGH.mdcrd
> rms first out eq_pro_hGH_rms_bef.out @CA,C,N
> center : 1-190
> image origin center familiar
> trajout eq_pro_hGH_reimage.mdcrd
> rms first out eq_pro_hGH_rms.out @CA,C,N
> radial rdf 0.5 10.0 :WAT_at_O
> strip : WAT
> strip : Na+

There should be no space between ":" and the residue names. Or you can use
quotation marks like ": WAT" or ': Na+'.

average avg.pdb pdb
> atomicfluct out out bfactor_eq_pro_bfactor.dat byatom bfactor
> trajout eq_pro_hGH_reima_strip.mdcrd nobox
>
>
> Trajectory file
> -rw-rw-r-- 1 dpandit dpandit 6442431278 Jun 10 15:30 eq_pro_hGH.mdcrd
>
>
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