AMBER Archive (2006)

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

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Sat Nov 11 2006 - 05:16:37 CST

Dear Case,

I try to add the size of box at the end of the rst file(90x90x90). But it
still has error so if i do it wrong so how to construct the rst file. Once i
try to construct rst file from mdcrd file (see input below)

this is the ptraj.in file

trajin mdcrd 100 100 1
trajout name.rst rst

but the format of generated rst file (more than 6 column of coordinate) is
not the same as standard rst (6 column). So, any help for this problem i
will thanks,

Jitrayut

---------- Forwarded message ----------
From: David A. Case <case_at_scripps.edu>
Date: พ.ย. 11, 2006 4:11 ก่อนเที่ยง
Subject: Re: AMBER: sander error: rst file crash
To: amber_at_scripps.edu

On Fri, Nov 10, 2006, jitrayut jitonnom wrote:
>
> 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

It doesn't look like you have any box information at the end of the restart
file, but this is required for periodic runs. You need to think about how
you
constructed the equil.rst file.

...good luck...dac

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