Re: FW: ammonia to methane/ c/o Jerome Henin

From: ehenriques_at_qui.uc.pt
Date: Mon Apr 26 2010 - 08:38:41 CDT

Hi Dale,

1) You need to add a chain name and a residue number to you pdb file, say:

CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1
ATOM 1 CT3 METHX 1 52.004 -12.697 -42.836 1.00 0.00
END

2) For the above pdb, and using your top_methane.inp, your psfCH4.pgn
should be:

package require psfgen
topology top_methane.inp
alias atom METH CT3 CB

segment X {pdb CH4.pdb}
coordpdb CH4.pdb X

guesscoord
writepdb mm.pdb
writepsf mm.psf
exit

That is, with the 'alias' you are renaming atom CT3 (from the pdb) to
CB (which is the name you gave it in your topology file). And, of
course, I'm invoking segment X (that's how I named it in the pdb).

Hope it helps.

E.

Quoting "Dale l. Schruben" <kfdls00_at_tamuk.edu>:

> The attached files (methane) that do not work where hacked together
> my me from the ammonia files. There are fields therein that are not
> covered in the tutorials, hence my hack. Any suggestions to get
> psfCH4.pgn running correctly would be appreciated. Dale
>
> ________________________________
>
> From: Dale l. Schruben
> Sent: Wed 4/7/2010 11:37 AM
> To: namd-l_at_ks.uiuc.edu
> Subject: ammonia to methane
>
>

------------------------------------------------------------------
Elsa S. Henriques e-mail: ehenriques_at_qui.uc.pt
Investigadora Auxiliar

Biologia Estrutural e Computacional (@CNC)
e Grupo de Qu=C3=ADmica Estrutural (@CCC)
Cv15 - RMB Lab
Departamento de Qu=C3=ADmica - Universidade de Coimbra
3004-535 COIMBRA Portugal

Tel.: +351 23 9852080 - ext.417
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