AMBER Archive (2006)

Subject: Re: AMBER: igb=2 and "bad atom type" conflict

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Wed Jul 05 2006 - 15:22:43 CDT

Hello Evan,

You will need to modify the AMBER source code to enter fluorine parameters.
I would go to $AMBERHOME/src/sander/mdread.f and add in parameters. Keep in
mind the vdw radius for fluorine is 1.47 Angstroms. Have fun and let me
know if you need any help with this.

Scott

On 7/5/06, Evan Kelly <ebkelly_at_ualberta.ca> wrote:
>
> Hi Everyone,
> I am trying to run a sander calculation on a protein ligand complex. I
> used antechamber to create the prmtop and inpcrd files for the ligand. I am
> using the igb=2 option. I get the following error:
>
> bad atom type: f
>
>
> here is my in file:
>
> &cntrl
> imin = 1,
> drms = 0.0001
> ntmin = 1,
> ncyc = 50,
> maxcyc = 100,
> ntb = 0,
> ntf = 1,
> ntc = 1,
> cut = 30,
> ntr = 0,
> igb = 2, saltcon= 0.1, rgbmax = 30, gbsa = 1,
> ntpr = 1, ntwx = 100, ntwr = 100,
> /
>
>
> Information of note:
>
> 1) a similar system that does not contain F atoms works perfectly fine.
> 2) I tried changing the 'f' atom types in the prmtop file to 'F' and the
> same problem occurred (bad atom type: F)
> 3) the error does NOT occur when I turn GB solvation off (igb = 0)
> 4) this was run on two different systems to the exact same error.
>
> Are there any suggestions or comments? Thanks in advance!
>
>
> ----------------------------------
> Evan Kelly
> ebkelly_at_ualberta.ca
>
>
>

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