AMBER Archive (2003)

Subject: Re: AMBER: leap/frcmod problem

From: David A. Case (case_at_scripps.edu)
Date: Wed Sep 17 2003 - 15:57:18 CDT

On Wed, Sep 17, 2003, Joseph Nachman wrote:
>
> -------------------------------------------------------------------
> frcmod.pty1
> --------------------------------------------------------------------
>
> MASS
> HH 10.08 hydroxyl group in protonated ASD,GLD (JN)

--> You need a blank line right here, to separate the BOND section from the
    MASS section

> BOND
> C -OS 320.0 1.290 PHOSPHOTYROSINE
> OH-HH 999.0 1.000 hydroxyl group in protonated ASD,GLD (JN)
>
> ANGLE
> CA-C -OS 35.0 124.71 PHOSPHOTYROSINE
> C -OS-P 100. 126.00 PHOSPHOTYROSINE
> C -OH-HH 100.0 113.00
> CT-OH-HH 100.0 108.50
>
>
> DIHE
> X -C -OS-X 2 1.800 180.000 2.000
>
> NONBON
> HH 0.6000 0.0157
>

> >> frcmod = loadamberparams frcmod.pty1
> Loading parameters: ./frcmod.pty1
> Reading force field mod type file (frcmod)
> ERROR: BOND: mass not read - omitting
> ERROR: C: mass not read - omitting
> (UNKNOWN ATOM TYPE: HH)

Note the above error messages: the program thinks that "BOND" is a new atom
type, etc.

..hope this helps...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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