Hi Dr. Bill,
Very amazing! Using the command you suggested, it work well now!
Very appreciated for your help!
Good weekend!
Rilei Yu
--- 10年5月1日，周六, Bill Miller III <brmilleriii.gmail.com> 写道：
发件人: Bill Miller III <brmilleriii.gmail.com>
主题: Re: [AMBER] Problem from ala scanning
收件人: "AMBER Mailing List" <amber.ambermd.org>
日期: 2010年5月1日,周六,上午7:08
You need to run the command line should look more like this:
$MMPBSA.py -i mmpbsa.in -sp complex_solvated.prmtop -cp complex.prmtop -rp
rec.prmtop -lp lig.prmtop -mc mutant_complex_prmtop -mr
mutant_receptor_prmtop -ml mutant_ligand_prmtop -y complex_md2.mdcrd
If you do 'MMPBSA.py --help' you will see the options for the command line
and what they mean.
Usage: MMPBSA.py {-O} -i inputfile \
-o output_file \
-sp solvated_prmtop \
-cp complex_prmtop \
-rp receptor_prmtop \
-lp ligand_prmtop \
-y mdcrd1 mdcrd2 mdcrd3 ... mdcrdN \
{-do decomp_output_file} \
{-yr receptor_mdcrd1 ... receptor_mdcrdN} \
{-yl ligand_mdcrd1 ... ligand_mdcrdN} \
{-mc mutant_complex_prmtop} \
{-mr mutant_receptor_prmtop} \
{-ml mutant_ligand_prmtop} \
{-srp solvated_receptor_prmtop} \
{-slp solvated_ligand_prmtop} \
{-make-mdins} || {-use-mdins} || {-compile-output}
You were excluding the flags for the mutant prmtops. If you specify the
&ala_scan section in your input, then the script will run the MMPBSA
calculation for the wild-type system and the mutant system in the same run.
Let me know if you have any more questions.
Good luck!
-Bill
On Fri, Apr 30, 2010 at 6:58 PM, Rilei Yu <yulaomao1983.yahoo.com.cn> wrote:
> Dear Dr. Bill,
>
> Thanks for your detailed reply! I have checked the top file as your
> suggestion. Unfortunately, I did not find any problem. And when I re-run
> tleap, I also did not any complain. So I run my job using two command line
> $MMPBSA.py -i mmpbsa.in -sp complex_solvated.prmtop -cp complex.prmtop
> -rp re.prmtop -lp lig.prmtop -y complex_md2.mdcrd (-68kcal/mol)
> $MMPBSA.py -i mmpbsa.in -sp complex_solvated.prmtop -cp
> mutant_complex_prmtop -rp mutant_receptor_prmtop -lp mutant_ligand_prmtop -y
> complex_md2.mdcrd (-57kcal/mol)
> If there is any problem with top file, why it can work well? Is there any
> problem with my command?
> Very thanks again!
> Rilei Yu
>
> --- 10年4月30日，周五, Bill Miller III <brmilleriii.gmail.com> 写道：
>
> 发件人: Bill Miller III <brmilleriii.gmail.com>
> 主题: Re: [AMBER] Problem from ala scanning
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 日期: 2010年4月30日,周五,下午10:52
>
> This means there is an inconsistency somewhere in your mutant topology
> files. The alanine mutation was only in the ligand, correct? So does that
> mean that receptor_prmtop and mutant_receptor_prmtop are the same files?
> Did
> tleap provide any errors or warnings when you were making the mutant
> prmtops? Have you checked both the mutant_complex_prmtop and the
> mutant_ligand_prmtop to make sure the correct residue was changed from LYS
> to ALA? The mutation should be present in *both* of these prmtops if the
> mutation is in the ligand. Without seeing the prmtops or the leap.log it is
> difficult to pinpoint the exact location of the problem. These are simply
> suggestions for you to try to find the error.
>
> Good luck! I hope this helps.
>
> -Bill
>
> On Fri, Apr 30, 2010 at 10:31 AM, Rilei Yu <yulaomao1983.yahoo.com.cn
> >wrote:
>
> > Dear amber users,
> >
> > When I try to perform ala scanning on my system, an error appeared in my
> > output file: WARNINGS: Invalid alanine scanning topology file(s)! It will
> > not be performed.
> > As a result, no mutational energy was calculated.
> >
> > I read the manual carefully, and try to delete the side chain of Lys to
> ALA
> > (only one mutation on the ligand). The name is also changed. Then the
> > mutant_ligand_prmtop, mutant_complex_prmtop and mutant_receptor_prmtop
> were
> > produced using leap. Can anyone tell what is wrong?
> >
> > I appreciated for your help!
> > Rilei Yu
> >
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Fri Apr 30 2010 - 17:00:03 PDT
