AMBER Archive (2006)

Subject: Re: AMBER: carnal prob

From: Stefano Federico Massimiliano Pieraccini (Stefano.Pieraccini) (Stefano.Pieraccini_at_unimi.it)
Date: Thu May 04 2006 - 02:58:18 CDT

Probably the '-' character is illegal in file names (in carnal use) , so it is not recogniseg. Try to use an underscore changing the filename and your input file.

Best regards

Stefano Pieraccini

----- Messaggio Originale -----
Da: bala
Data: Giovedi', Maggio 4, 2006 9:48 am
Oggetto: AMBER: carnal prob
A: amber_at_scripps.edu

> dear amber users,
>
> i wanted to use hbond analysis in carnal. I am using Amber8. i
> hve pasted below my input and output file. Kindly suggest me
> what could be the problem. i hve checked the path of topology
> file and co-ord file. everything is correct.
>
> input
> -------------------------------------------------------
> FILES_IN
> PARM p1 at-oct.prmtop;
> STREAM s1 traject/vp1.mdcrd.gz;
> FILES_OUT
> HBOND h1 accpt LIST;
> HBOND h2 Donr LIST;
> DECLARE
> GROUP g1 (RES 10);
> GROUP g2 (RES 25-5223);
> OUTPUT
> HBOND h1 DONOR g2 ACCEPTOR g1 STATS;
> HBOND h2 DONOR g1 ACCEPTOR g2 STATS;
> END
> ---------------------------------------------------------------
> output
> ---------------------------------------------------------------
> - CARNAL -
> AMBER 8.0
> COORDINATE ANALYSIS
>
> input stdin
> > # HBOND analysis
> > FILES_IN
> > PARM p1 at-oct.prmtop;
> Reading parm file (at)
> parm: opening at
> at: does not exist (nor do .Z or .gz)
> ---------------------------------------------------------------
>
> thanks in advance,
> c.bala
>
>

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