Hi Scott,
Thanks for the tip. Just to make sure I understand the code and the
data storage in AMBER (I've never had to modify this code before):
1) For the parameters I have used, I need to add F parameters in the
section starting at line 1054 of mdread.f, "if ( gbsa == 1 ) then"?
2) I should add a line like:
else if (atype == 'F' .or. atype == 'f') then
x(l165-1+i) = 1.47d0 + 1.4d0
x(l170-1+i) = 0.68563d0
x(l175-1+i) = -0.1868d0
x(l180-1+i) = -0.00135573d0
x(l185-1+i) = 0.00023743d0
into the series of elseif statements? The l165 parameter is the vdw
radius "augmented by 1.4 Ang.". However, I have no idea what the
other parameters stand for or what they should be for F. Any
suggestions?
3) I should only need to recompile the sander code, by "make serial"
in $AMBERHOME/src/sander/, right?
Please let me know if I'm on the right track. Thanks!
On 5-Jul-06, at 2:22 PM, Scott Pendley wrote:
> 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.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.ualberta.ca
>
>
>
--------------------------------
Evan Kelly
ekelly9.gmail.com
----------------------------------
Evan Kelly
ebkelly.ualberta.ca
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Received on Sun Jul 09 2006 - 06:07:14 PDT
