Hi Scott,
So, parameters I160-185 don't contribute significantly to surface
area calculations? Thanks again for the help! I'll let you know how
it turns out...
On 6-Jul-06, at 9:47 AM, Scott Pendley wrote:
> You are on track. I would leave lines 3-7 (I170-I185)set to
> 0.00000 unless you actually know the parameters. If I remember
> correctly remember they related to a complex equation for
> calculating surface area with overlapping atoms. You will probably
> want to alter sections for both igb=1 and igb=2.
>
> On 7/5/06, Evan Kelly <ekelly9.gmail.com> wrote:
> 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
