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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>
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Received on Fri Apr 30 2010 - 16:00:03 PDT
