Hi Amanpreet,
I am attaching a sample prmtop and pointing you to the residue number.
Please check that number in your prmtops.
*CHUNK of SAMPLE PRMTOP:*
%FORMAT(10I8)
55347 21 53284 2126 4612 2892 9307 8907 0
0
91037 *17352* 2126 2892 8907 93 209 198 51
1
0 0 0 0 0 0 0 1 24
0
0
%FLAG ATOM_NAME
---------------------------------------------------------------------------------------------------------
The bold one in the prmtop file is the residue number. Please make sure
your complex nres = receptor nres + ligand nres
The other way around is that you can use ante-MMPBSA.py to generate the
initial prmtop files from the solvated complex prmtop. You can type the
command line inputs as follows:
ante-MMPBSA.py -p solv_complex.prmtop -c dry_complex.prmtop -s :ions, water
(not the important metal ion(s), if any)
ante-MMPBSA.py -p solv_complex.prmtop -c receptor_dry.prmtop -s
:ions,water,ligand
ante-MMPBSA.py -p solv_complex.prmtop -c ligand_dry.prmtop -s "!(:ligand)"
Hope, this may help you to resolve your problem.
Best,
Satyajit
------------------------------
*From:* AMANPREET KAUR <akaur_phd21.thapar.edu>
*Sent:* Monday, June 19, 2023 11:04:14 AM
*To:* SATYAJIT KHATUA <
satyajitkhatua09.gmail.com>
*Subject:* Re: [AMBER] Error while running mmpbsa
Thank you sir for your response.
I have not used ante-MMPBSA.py to strip off any atoms or residues.
I have given the topology files which were generated using tleap and
antechamber commands for receptor and ligand respectively and mentioned in
the script of mmpbsa. But still the error persists.
Can what are the commands to check the no. of residues in a file.
Also plz share the steps or script before running mmpbsa and what to keep
in mind to obtain free energy calculations..
On Mon, Jun 19, 2023 at 10:44 AM SATYAJIT KHATUA <satyajitkhatua09.gmail.com>
wrote:
Hi Amannpreet,
Your log reads "PrmtopError: Complex nres !=
receptor nres + ligand nres".
Check carefully if your complex residue number equal to receptor residue
number + ligand residue number from the respective prmtop file.
If you used ante-MMPBSA.py to extract those check carefully the stripping
phase of the complex, receptor and ligand prmtop generation.
Best,
Satyajit
Get Outlook for Android <
https://aka.ms/AAb9ysg>
------------------------------
*From:* AMANPREET KAUR via AMBER <
amber.ambermd.org>
*Sent:* Monday, June 19, 2023 10:31:16 AM
*To:* amber.ambermd.org <amber.ambermd.org>
*Subject:* [AMBER] Error while running mmpbsa
Hlo
I am running mmpbsa in amber 20 using the following command
*MMPBSA.py -O -i mmpbsa.in <
http://mmpbsa.in/> -o mmpbsa.out
-cp solv_8e1x_noh.com <
http://solv_8e1x_noh.com/>.prmtop
-rp 8e1x_noh.prmtop -lp 8480_10.3_opt_chim.prmtop -y *nc*
But I am encountering an error which says "PrmtopError: Complex nres !=
receptor nres + ligand nres.
How to rectify this kindly help as I am badly stuck in this.
Thank you.
Regards
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Received on Sun Jun 18 2023 - 23:30:03 PDT
