The pdb indicates that it is MN, but I remove MN from display" File "/mnt/disk1/software/AMBER18/amber18/bin/MMPBSA-1.py", line 100, in <module><br/> app.run_mmpbsa()<br/> File "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa<br/> self.calc_list.run(rank, self.stdout)<br/> File "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run<br/> calc.run(rank, stdout=stdout, stderr=stderr)<br/> File "/mnt/disk1/software/AMBER18/amber18/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 157, in run<br/> self.prmtop))<br/>CalcError: /mnt/disk1/software/AMBER18/amber18/bin/sander failed with prmtop com-3.prmtop!<br/>Exiting. All files have been retained."<br/>I don't know how to solve this problem. Can you help me?<br/>Thanks
From: David A Case via AMBER <amber.ambermd.org>
Date: 2023-07-07 23:57:59
To: Riran <2115391084.st.gxu.edu.cn>,AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Error while running mmpbsa>On Fri, Jul 07, 2023, Riran via AMBER wrote:
>
>>I tried what you suggested, but it didn't work out. I tried MN , Mn2+, Mn,
>>but none of them worked.
>
>Use (for example) ambpdb to create a pdb file for your system, and see what
>the residue names are in your particular system. The PDB (and Amber)
>standard is to use MN as the residue name for manganese.
>
>Aside: you use of Na+ and Cl- is also non-standard: the correct names are NA
>and CL. I'm not sure you you prepared the system to get these names. (This
>is a curse of backwards-compatibilty: in the previous millenium, after the
>deluge but before the internet, Amber developers started using Na+ and Cl-.
>We somewhat foolishly tried to keep this as an alternative (for just these
>two ions plus K+), but that inevitably leads to confusion.)
>
>....dac
>
>
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Received on Tue Jul 11 2023 - 20:30:02 PDT
