AMBER Archive (2008)

Subject: Re: AMBER: PTRAJ - Segmentation Fault

From: dpandit_at_brandeis.edu
Date: Wed Jun 11 2008 - 12:48:54 CDT

Hi Jianyin,
Thank you for your suggestion but even after making the change I still
got the segmentation fault. Based on AMBER archive messages I also
removed radial calculation but still the same problem. Here is the
edited file.

THX
Deepa

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
strip :WAT
strip :Na+
average avg.pdb pdb
atomicfluct out out bfactor_eq_pro_bfactor.dat byatom bfactor
trajout eq_pro_hGH_reima_strip.mdcrd nobox

Quoting Jianyin Shao <jyshao2004_at_gmail.com>:

> 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
>>
>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo_at_scripps.edu
>>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu