AMBER Archive (2006)

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

From: Evan Kelly (ebkelly_at_ualberta.ca)
Date: Wed Jul 05 2006 - 14:25:16 CDT

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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