Hi,Bill,thank you
so far,I can only master the mm_pbsa.pl script.You have told me how to set the parameters of the extracting step.Now do I need change anything of the following binding calculation input file to fit my no water system to generate the accurate binding energy result? I read from the explaination that some items is used to set the solvent effect,for example, "EXDI - Dielectric constant for the surrounding solvent".In fact,I am not familiar with these even I study carefully of every item.
so,can you kindly tell me how to change these parameters if it is necessary,of courese,except the prmtop file.
really appreciate your help.
.GENERAL
PREFIX snapshot
PATH ./
COMPLEX 1
RECEPTOR 1
LIGAND 1
COMPT ./ras-raf.prmtop
RECPT ./ras.prmtop
LIGPT ./raf.prmtop
GC 0
AS 0
DC 0
MM 1
GB 1
PB 1
MS 1
NM 0
.PB
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2
LINIT 1000
PRBRAD 1.4
ISTRNG 0.0
RADIOPT 0
NPOPT 1
CAVITY_SURFTEN 0.0072
CAVITY_OFFSET 0.00
SURFTEN 0.0072
SURFOFF 0.00
.MM
DIELC 1.0
.GB
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
SURFTEN 0.0072
SURFOFF 0.00
.MS
PROBE 0.0
.PROGRAMS
2010-04-18
geyan
发件人： Bill Miller III
发送时间： 2010-04-18 21:20:18
收件人： AMBER Mailing List
抄送：
主题： Re: [AMBER] how do MM_PBSA without water
Simply adding 'intial_traj=1' in the &general namelist of the MMPBSA.py
input file will take care of this for you.
This isn't much more complicated using mm_pbsa.pl either. In the @MAKECRD
section make sure you set 'BOX' as 'NO' and then just fill in the rest of
the information as explained in the AMBER Manual (start frame, end frame,
ligand atom numbers, receptor atom numbers, etc). Note that this section is
only used when generating snapshots (GC) is turned on (i.e. set to 1).
Good luck!
-Bill
On Sun, Apr 18, 2010 at 3:48 AM, geyan <geyan.big.ac.cn> wrote:
> Dear Amber users,
> I have got the trajectory of a system of DNA-Protein complex. Because I
> konw they'are interacting with each other without water in nature,so I
> didn't add solvent effect.Now the problem is,how I alter the script from the
> Amber Tutorial of MM_pbsa to extract snapshot and do the accurate PBSA
> analysis.The standard input of the two scripts is a little too complex for
> me to change,it has beyond my scope.
> Any help is appreciated
>
>
> 2010-04-18
>
>
>
> geyan
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Apr 18 2010 - 08:30:02 PDT
