I tried to calculate the binding free energy of a protein with it's ligand
with mm/pbsa.
My mm/pbsa script is:
*##################################################
.GENERAL
#
PREFIX pro
PATH ./snapshots
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../pro_com.prmtop
RECPT ../protein.prmtop
LIGPT ../pro.prmtop
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 0
MS 0
#
NM 0
.MM
DIELC 1.0
.GB
IGB 2
GBSA 2
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
SURFTEN 0.0072
SURFOFF 0.00
###############################################*
And there is a bromide in my ligand molecule.The output message is:
* bad atom type: Br
/usr/amber9/exe/sander -O -i sander_com.in -o sander_com.1.out -c
./snapshots/pro_com.crd.1 -p ../pro.prmtop not successful*
Is there missing parameters for bromide when calculating binding energy
using mm/pbsa?
2009/9/28 Ray Luo <ray.luo.uci.edu>
> Please be more specific on where you saw this message. Inclusion of your
> input file, log file, and so on would be very helpful.
>
> All the best,
> Ray
>
> ==========================================
> Ray Luo, Ph.D.
> Associate Professor
> Dept Molecular Biology & Biochemistry
> University of California, Irvine, CA 92697
> USPS: PO Box 3900 Email: rluo.uci.edu
> Phones: (949) 824-9528, 9562
> Web: http://rayl0.bio.uci.edu/
> ==========================================
>
>
>
> Baifan Wang wrote:
>
>> *Hello all,
>>
>> I'm trying to do mm/pbsa calculation about a protein with it's ligand
>> which
>> has a bromide,then I got a message : bad atom type Br.
>> **Can somebody tell me how to solve this problem?
>> *
>> Best regards
>>
>> Baifan wang.
>> *
>> **
>> *
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>
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Received on Mon Sep 28 2009 - 00:30:01 PDT
