Hi Dwight,
No, gbsa=2 is not set, but, yes, I am doing energy decomposition.
Here is the input file:
Input file for running GB
&general
verbose=2, strip_mdcrd=1, strip_mask=":WAT",
entropy=0, startframe=62, endframe=10000, interval=62
/
&decomp
idecomp=2, dec_verbose=3,
/
&gb
igb=5, saltcon=0.150
/
&pb
istrng=0.150
/
&nmode
nmstartframe=8, nmendframe=160, nminterval=6,
maxcyc=50000, drms=0.0001, nmode_igb=1, nmode_istrng=0.1,
/
Thanks for your help.
Rami
On Feb 28, 2012, at 6:33 PM, Dwight McGee wrote:
> Hi,
>
> Is gbsa=2 in your input? Are performing an energy decomposition analysis?
>
> On Tue, Feb 28, 2012 at 5:59 PM, Osman, Roman <roman.osman.mssm.edu> wrote:
>
>> Greetings,
>>
>> I am running an mmpbsa_py on a complex with a small molecule that contains
>> Br.
>> I am getting this error:
>>
>> Beginning GB calculations with sander...
>> calculating complex contribution...
>> bad atom type: br
>>
>> I assume the error is because of the Br.
>> I would be grateful if you suggest how to fix this problem.
>> Thanks very much,
>>
>> Roman Osman
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> T. Dwight McGee Jr.
> Quantum Theory Project
> University of Florida
> Graduate Student
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 28 2012 - 16:30:02 PST
