AMBER Archive (2009)

Subject: Re: [AMBER] problem when doing mm/pbsa: bad atom type Br

From: Baifan Wang (ferlich.wang_at_gmail.com)
Date: Mon Sep 28 2009 - 02:26:06 CDT

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_at_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_at_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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>>
>>
>>
>
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