AMBER Archive (2005)

Subject: Re: AMBER: Can GB and MS work correctly together in mmpbsa?

From: zhli_2000_at_126.com
Date: Sat Jul 16 2005 - 22:30:47 CDT

Thank you for the advice. I have put the atom radium of F in the
mm_pbsa_calceneent.pm. Then I run the following :

--------------------------------------------------------------------
PREFIX min_cyc16
PATH ./
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ./mincomplex.top
RECPT ./ppo.top
LIGPT ./cyc16.top
#
GC 0
AS 0
DC 1
#
MM 1
GB 1
PB 0
MS 0
#
NM 0
#
-------------------------------------------------------------------
The error message is still :
   bad atom type: F

When I switch MS=0 to MS=1, the error message is:
    Checking sanity
    Checking GENERAL
    Energy decomp is not (yet) possible with GC, AS, NM, PB, MS

So I don't know how to deal with this. Which input file can be run
correctly?

---------------------------------------------------------------------------- 

---

On Fri, 15 Jul 2005 14:08:43 -0600, Scott Pendley <scott.pendley_at_gmail.com> 
wrote:

> As a follow up to my last note.  Specifically you should modify the
> generate_pqr() section of mm_pbsa_calceneent.pm.  This is the
> modification I added to my code . . .
>
> "Na+"  => 1.200 + 1.400,
> 		 "Cl-"  => 1.700 + 1.400,
> 		 "MG"   => 1.180 + 1.400,
> "F"    => 1.470 + 1.400,
> 		);
>
> Have fun with this...
>
>
> On 7/15/05, Scott Pendley <scott.pendley_at_gmail.com> wrote:
>> That is because you have not put in the parameters of F for the
>> molsurf program.  It is similiar to doing to the modification you did
>> earlier.  If you run into trouble doing this let me know and I will
>> show you how I did it.
>>
>> On 7/15/05, zhli_2000_at_126.com <zhli_2000_at_126.com> wrote:
>> > Hi,
>> >   Thank you for the explanation. But Because there is an atom F in the
>> > ligand, when I switch MS=1 to MS=0, mmpbsa cann't work correctly. The 
>> error
>> > message is:
>> > bad atom type: F
>> >
>> > What should I do?
>> > Thank you!
>> >
>> >
>> > >
>> > > If you switch MS=1 to MS=0, it should work. Energy decomposition 
>> does not
>> > > work so far with a SAS calculation based on MS, but relies on 
>> another
>> > > method approximating atomic surfaces starting from icosahedra.
>> > > Best regards
>> > >
>> > > Holger
>> > >
>> > >>
>> > >
>> >
>> >
>> >
>> >
>> >
>> >
>> > ----------------------------------------------------------------------- 
>>
>>
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