AMBER Archive (2006)

Subject: Re: AMBER: saveamberparams error in Amber9

From: Weihua Li (whli.ecust_at_gmail.com)
Date: Thu Jun 15 2006 - 01:48:52 CDT

 Thanks Dav, I extended the equivalence list by adding NP, NO to N and CX to
C* in parm99.dat. It does work.
But when I use the second method that creates the vdW parameters in my
frcmod file, I have to add the NP, NO,CX into addatomtypes{} in
leaprc.ff03 to make it work.
So I wonder why it is not necessary to add the NP, NO,CX into
leaprc.ff03when using the first method. To my knowledge, it's only
using the vdW
parameters equivelent to N and C, rather than adding the atom type.

Regards,
weihua

These heme parameters were developed long before ff03. Basically,
> parm94.dat
> defines van der Waals parameters for NP, NO, CX, but parm99.dat (from
> which
> ff03 was developed) does not. So, you will need to copy the van der Waals
> parameters from parm94.dat into your frcmod file if you want to use ff03
> as the rest of the force field.
>
> Note that in parm94.dat, NP and NO are equivalenced to "N", and CX is
> equivalenced to "C". So, you will either need to extend the equivalence
> list
> in parm99.dat (simplest solution), or create the necessary vdW parameters
> in
> your frcmod files.
>
> ...good luck....dac
>
>

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