Dear Amber_users,
I agree that the system is too big.
I tried with CA,C and N atoms but no luck! Here is my script. Your input is
appreciated.
--------------------------------------------------------
trajin prod36.mdcrd 1 50 10
trajin prod37.mdcrd 1 50 10
trajin prod38.mdcrd 1 50 10
trajin prod39.mdcrd 1 50 10
trajin prod40.mdcrd 1 50 10
trajin prod41.mdcrd 1 50 10
trajin prod42.mdcrd 1 50 10
rms first .CA,C,N
matrix mwcovar name comp.matrix :1-1471.CA,C,N
analyze matrix comp.matrix out complex_entropy.out thermo reduce
matrix mwcovar name rec.matrix :1-894.CA,C,N
analyze matrix rec.matrix out receptor_entropy.out thermo reduce
matrix mwcovar name lig.matrix :895-1471.CA,C,N
analyze matrix lig.matrix out ligand_entropy.out thermo reduce
On 26 October 2011 16:56, Collu, Francesca (DCB) <
francesca.collu.dcb.unibe.ch> wrote:
> Hello!
>
> I had the same problem and I discovered that my system is too big and my
> computer does not have
> enough memory for such big system.
>
> Now I am doing the calculation considering just CA atoms and not all the
> atoms.
>
> regards
>
> Francesca
> ________________________________________
> Von: Neha Gandhi [n.gandhiau.gmail.com]
> Gesendet: Mittwoch, 26. Oktober 2011 10:50
> Bis: AMBER Mailing List
> Betreff: [AMBER] quasi-harmonic analysis
>
> HI,
>
> I am using AMBER 11 and Ambertools 1.5. I am trying to run entropy
> calculations using quasi-harmonic appoximation. I get similar errors as
> reported earlier (http://archive.ambermd.org/201108/0152.html). The
> entropy
> is zero. I couldn't find any errors in output files. Unfortunately, I
> cannot
> attach input files here due to their size.
>
> Awaiting your positive reply,
>
> Regards,
> Neha Gandhi
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>
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>
--
Regards,
Neha Gandhi,
School of Biomedical Sciences,
Curtin University of Technology,
GPO Box U1987 Perth,
Western Australia 6845
Phone: 9266 9061
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Received on Wed Oct 26 2011 - 03:00:06 PDT
