Dear AmberUSers,
I am working on a metal binding protein with 230 Aa. For the metal binding
sites, I have performed gaussian calculations and have derived the RESP charges.
I have followed the following Amber tutorial
(
http://ambermd.org/tutorials/advanced/tutorial1_adv/) to build in the library
files for the modified residues. However, I am not able to generate the frcmod
file for the missing parameters. I read in the AMBER manuals that parmchk can be
used to generate frcmod files. To use parmchk i saved the mol2 file of my
structure using saveMol2 command in leap. The mol2 file is attached with this
mail. The mol2 file was then used as an input to parmchk. The command that I
used is :
> parmchk -i apo1_H.mol2 -o apo.frcmod -f mol2 -p
/$AMBERHOME/dat/leap/parm/parm99.dat
On doing this, I get segmentation fault on a normal desktop. I tries using it in
a cluster and the program just hangs up. On firing "top", i can see that parmchk
is running, but does not seem to be giving any output.
Will parmchk work on a system as huge as 230 aa.
Will the presence of metal effect its performance, like antechamber (antechamber
does not work with metals)
I used check unit command in leap to see the missing parameters. It says that
only some bond length and angles are missing. Is it ok if i run a small script
which calculats the bond length and angle from the PDB coordinates and manually
create an frcmod file.
Thank you.
Cheers
Soma
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Received on Tue Nov 22 2011 - 04:00:03 PST
