AMBER Archive (2007)

Subject: Re: AMBER: error in modified PNA -DNA simulation..

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Thu Oct 11 2007 - 19:26:11 CDT

Hi,

On Wed, 10 Oct 2007, Sharad gupta wrote:

> I am trying to simulate modified PNA- DNA .
> PNA ( in which the whole phosphodiester backbone of DNA is replaced with 2-Aminoethylglycine backbone.)
> Modified PNA (adenine base is also modified ).
>
> I have stuck with an error
>
> Id.so.1: sander: fatal: libsunperf .so. 2: open failed No such file or directory
> /opt/age/default/spool/tentacle6/job_scripts/1101: line 5: 10035 killed
> $AMBERHOME/exe/sander –o -i wat_nsd_md3.in -o wat_nsd_md3.out -p wat_nsd.prmtop -c wat_nsd_md2.rst -r wat_nsd_md3.rst -ref wat_nsd_md2.rst -x wat_nsd_md3.mdcrd

The identity of the unavailable file is not clear from this snippet.
You mention below that you have successfully used sander.
This smells like a simple oversight:
Did you try a short interactive run to validate your inputs and script ?
I have not studied your input file.

Scott

> My input file wat_nsd_md3.in is
>
> nsd 15-mer: 10ps MD with res(10.0) on nsd
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 1,
> cut = 10,
> ntr = 1,
> ntc = 2,
> ntf = 2,
> tempi = 0,
> temp0 = 300.0,
> ntt = 3,
> gamma_ln = 1,
> nstlim = 5000, dt = 0.002,
> ntpr = 250, ntwx = 250, ntwr = 10000
> /
> Hold the nsd fixed
> 10.0
> RES 1 16
> END
> END
>
>
> Charges on PNA backbone taken from reference JACS, 1998, 120, 5895-5904
> But the charge on modified base is calculated from gaussian (03W).
> I have got reliable results in case of normal PNA-DNA simulation with the same input files.
> any body help me why this is happened in case of modified PNA.
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