AMBER Archive (2006)

Subject: Fwd: AMBER: sander error: rst file crash

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Fri Nov 10 2006 - 09:52:00 CST

Dear Carlos,

I am using amber version 9 and the inpcrd file is generated from the
equilibrium step (equil.in). Actually, i do the mm-pbsa according to the
mm-pbsa tutorial (advance tutorial).

Jitrayut

---------- Forwarded message ----------
From: Carlos Simmerling <carlos_at_csb.sunysb.edu>
Date: พ.ย. 10, 2006 8:26 หลังเที่ยง
Subject: Re: AMBER: sander error: rst file crash
To: amber_at_scripps.edu

- where did the inpcrd file come from?
- what sander version are you using?
these might help us give you an answer.

jitrayut jitonnom wrote:

> Dear amber users,
>
> I have a problem when i try to begin sander after job die. It show
> error at the end of out file which show here below:-
>
> equil2.out
>
> Here is the input file:
>
> heat ras-raf
> &cntrl
> imin=0,irest=1,ntx=5,
> nstlim=148000,dt=0.002,
> ntc=2,ntf=2,
> cut=8.0, ntb=2, ntp=1, taup=2.0,
> ntpr=1000, ntwx=1000,
> ntt=3, gamma_ln=2.0,
> temp0=300.0,
> /
>
>
>
--------------------------------------------------------------------------------
> 1. RESOURCE USE:
>
--------------------------------------------------------------------------------
>
> | Flags:
> getting new box info from bottom of inpcrd
> | INFO: Old style inpcrd file read
>
> peek_ewald_inpcrd: SHOULD NOT BE HERE
>
>
>
> and the end of rst file is shown here:
>
> equil.rst
>
> end of file
>
> 0.1158442 0.0034209 -0.1880667 -0.2611832 0.6159938 0.0356480
> -0.1702497 0.0834863 -0.0236473 0.0219285 -0.0337172 0.0520130
> -0.2057171 0.0938851 0.4554208 0.1215038 -0.4387970 -0.1657079
> -0.2094962 -0.0511841 -0.1332011 0.2905402 0.5463824 -0.3891711
> -0.4897937 -0.5227692 -0.0726845 -0.1418198 -0.0038642 0.1778031
> 0.2470789 -0.1056579 -0.1661152 1.0015408 -0.4809184 0.0302057
> -0.2518932 0.1004485 0.1605738 -0.9706663 -0.8502000 -0.0749598
> -0.4526771 -0.1580437 0.1467325 -0.0083844 0.1081232 0.1225735
> 0.2637010 -0.7594001 0.5247114 -0.2783051 0.8794519 -0.2053294
> -0.2813098 0.1164523 -0.2792391 0.5998864 0.6746857 -0.2420203
> 0.4517652 -0.8129144 -0.3797197 0.1574909 -0.0732390 0.0087053
> -0.0653241 -0.0394696 0.2901497 0.0858859 -0.1262879 0.0460561
> -0.3345731 -0.2164283 -0.4103812 0.0138714 0.5943789 -0.4453507
> -0.3056044 -0.2171315 0.4107326 -0.0049606 -0.1484431 -0.0739576
> -0.2638457 0.0315161
>
>
>
> So, my question is how to obtain the right rst file in order to run
> sander ?
>
> Any helps will be thanks,
>
> Jitrayut Jitonnom, Ph.D.(candidate)
> Dept. of Chemistry,
> Computational Simulation,
> and Modeling Laboratory (CSML),
> Chiang Mai University, Thailand.
> Tel: +66(0)6613-4218
> Email: jitrayut.018_at_gmail.com <mailto:shafinaz_at_bri.nrc.ca>
>

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