You may consider trying to use MCPB to parametrize your metal complex.
On Nov 22, 2011, at 6:42 AM, "Soma Ghosh" <soma.mbu.iisc.ernet.in> wrote:
> 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.
The small script will most likely not work. The equilibrium bond and angle values are only half of the necessary parameters (the easy half). You also need force constants for each angle and bond type.
Likewise, you also need dihedral parameters which also requires much more than simple geometrical measurements. So unless your script will scan databases or calculate the necessary parameters besides just the lengths and angles your script won't be enough.
HTH,
Jason
>
> Thank you.
>
> Cheers
> Soma
>
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--
Jason Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Nov 22 2011 - 04:30:05 PST
