AMBER Archive (2006)

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

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Sat Nov 11 2006 - 06:38:52 CST

you need to use the right syntax for the trajout command.
check the ptraj section of the amber manual.

jitrayut jitonnom wrote:

> 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 <http://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 <mailto: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 <mailto: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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