-

Re: Sobtop

dummy@example.com (sobereva) — Tue, 22 Oct 2024 06:51:38 +0000

Dummy atom is irrelvant to sobtop. Only real atoms can occur in the topology file created by sobtop.

Re: Sobtop

dummy@example.com (gottlib) — Mon, 21 Oct 2024 18:42:49 +0000

Hello
Is it possible to continue this topic regarding sobtop here?
Is there any way to add a dummy atom to simulate a virtual wall? Do I need just to modify itp file of GAFF?
Thanks

Re: Sobtop

dummy@example.com (sobereva) — Fri, 24 Nov 2023 18:29:05 +0000

Please note that Mulliken has poor reproducibility of molecular electrostatic potential and thus should never be used for molecular dynamics purpose. See comparison of reproducibility of various atomic charges (Table 5 in http://www.whxb.pku.edu.cn/CN/abstract/ … 818.shtml).

There is no way currently. Please enter sobtop folder first before using it.

Re: Sobtop

dummy@example.com (gottlib) — Fri, 24 Nov 2023 14:56:51 +0000

Thanks for answering
I could make a script which could be useful to prepare .chg file for sobtop using Mulliken charges generated in Orca. If you want I can share it with you.
Is there any way to include .ini file into bash shell to perform sobtop from any folder?

Thanks

Re: Sobtop

dummy@example.com (sobereva) — Wed, 15 Nov 2023 00:28:18 +0000

Just copy Mulliken charges into [atoms] section of the .itp file generated by sobtop.

Sobtop

dummy@example.com (gottlib) — Tue, 14 Nov 2023 21:54:27 +0000

Hello
Is there a way to put Mulliken partial charges generated in Orca into .chg file for sobtop? I would like to compare is there any change in self-assembly depending on charge scheme, Mulliken or RESP.

Thanks in advance