Hi,
This was quite helpful. It solved the issue, thanks. I also tried
mentioning the water model to use using "water_model" in MCPB.py, AMBER22
it still would give the same error. Luckily I had access to an older
version of AMBER, using it fixed the issue. I hope there is some way to get
this working in AMBER22 as well. But my problem is solved for now.
Regards
Abhilash
On Tue, Jun 20, 2023 at 5:17 AM Huang ZiJian <Hzj-0820.outlook.com> wrote:
> Hi,
> I also encountered the same problems. After retrieving information from
> the email list, using an old version of AMBER (such as AMBER18 or 16) could
> help (http://archive.ambermd.org/202107/0163.html). I guess this is due
> to the default ”water_model“ is "OPC" in MCPB.py of AMBER22.
>
> Regards,
> Zijian
> ------------------------------
> *发件人:* Abhilash J via AMBER <amber.ambermd.org>
> *发送时间:* 2023年6月20日 11:53
> *收件人:* AMBER <amber.ambermd.org>
> *主题:* [AMBER] Error in modelling with ion using MCPB.py
>
> Hi,
>
> I am having an issue modelling with ion using MCPB.py. The error might
> be with the water molecule atom type (OW). I am unable to understand the
> reason for it. I checked the WAT.mol2 file and it seems fine. This occurs
> after I run the gaussian calculations and issue the command:
> MCPB.py -i PROT.in -s 2
>
> ==============================================================
> Atoms which has changed the atom types: [259, 548, 2681, 2684, 2706, 2726,
> 2729]
> 17-SER.259-OG : OH --> Y1
> 35-THR.548-OG1 : OH --> Y2
> 169-MG.2681-MG : MG --> M1
> 170-GTP.2684-O3G : o --> Y3
> 170-GTP.2706-O3B : o --> Y4
> 171-WAT.2726-O : OW --> Y5
> 172-WAT.2729-O : OW --> Y6
> Traceback (most recent call last):
> File "/programs/x86_64-linux/amber/22/bin/MCPB.py", line 665, in <module>
> gene_pre_frcmod_file(ionids, premol2fs, stpdbf, stfpf, smresf, prefcdf,
> File
>
> "/programs/x86_64-linux/amber/22/lib/python3.10/site-packages/pymsmt/mcpb/gene_pre_frcmod_file.py",
> line 132, in gene_pre_frcmod_file
> print('YES', atyp2 + massparms[atyp1], file=fmf)
> KeyError: 'OW'
> =========================================================
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>
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Received on Mon Jun 26 2023 - 17:00:02 PDT
