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nakul20

Member

Registered: 2020-08-13

Posts: 6

"Error encountered while loading atom in this file" - EDA-FF

Hello,

I get the following error while trying to run an EDA-FF analysis:

"Error encountered while loading atom in this file!"

I'm trying to use the Universal Force Field (UFF). This happens when I try to load the atomic charges and types.

Any help would be much appreciated!

Thank you

nakul20

Member

Registered: 2020-08-13

Posts: 6

Re: "Error encountered while loading atom in this file" - EDA-FF

Just adding to my comments above - while using the UFF, can I specify the atom type as 'UF' for all the atoms?

Last edited by nakul20 (2020-08-13 02:58:51)

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,768

Website

Re: "Error encountered while loading atom in this file" - EDA-FF

I cannot give you detailed advice since I don't have your input file. Probably the format of your input file is problematic. Before studying your system, please fully reproduce the example in the Multiwfn to guarantee that your operation steps are correct.

If you simply want to use UFF forcefield, only atomic charges should be given in the molecular file, because UFF defined only one atomic type for each element, thus you do not need to explicitly specify atom types.

nakul20

Member

Registered: 2020-08-13

Posts: 6

Re: "Error encountered while loading atom in this file" - EDA-FF

Thanks for the prompt reply, I appreciate it.

I did try to reproduce it and it worked.

The structure file I load is a PDB file like this:

ATOM 515 4H54 MOL 2 9.449 28.801 25.803 1.00 27.40 H
ATOM 516 5H54 MOL 2 10.702 28.949 24.819 1.00 27.40 H
ATOM 517 6H54 MOL 2 9.249 28.650 24.222 1.00 27.40 H
ATOM 518 Pd54 MOL 2 10.279 18.052 11.677 1.00 8.86 Pd2+

I get the following error: Error encountered while loading atom 517 in this file!

My molecule.txt (where the charges and types are written) was like this:

-0.45
0.138
0.15
0.145

This gives an error.

Now, it is like this:
UF -0.45
UF 0.138
UF 0.15
UF 0.145

This worked for me.

But, is this correct?

I look forward to hearing from you soon.

Thank you!

Last edited by nakul20 (2020-08-13 13:33:58)

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,768

Website

Re: "Error encountered while loading atom in this file" - EDA-FF

Have you switched forcefield to UFF via option -1? If you haven't, you should do this, and then you do not need to write UF in molecular file.

nakul20

Member

Registered: 2020-08-13

Posts: 6

Re: "Error encountered while loading atom in this file" - EDA-FF

Thank you! That worked - I forgot to change the forcefield option

nakul20

Member

Registered: 2020-08-13

Posts: 6

Re: "Error encountered while loading atom in this file" - EDA-FF

Also, I had another question:

So, when -1 = UFF and molecule.txt is like this:

-0.45
0.138
0.15
0.145

and, when -1 = AMBER99 & GAFF and molecule.txt file is like this:

UF -0.45
UF 0.138
UF 0.15
UF 0.145

I get different answers for both cases. I should be getting the same answer, correct?

I look forward to hearing from you soon.

Thank you!

Last edited by nakul20 (2020-08-16 01:14:16)

sobereva

Tian Lu (Multiwfn developer)

From: Beijing

Registered: 2017-09-11

Posts: 1,768

Website

Re: "Error encountered while loading atom in this file" - EDA-FF

The former case should be correct, namely not only parameters of UFF will be used, but also the interaction will be calculated in the way of UFF. Note that UFF employs different mixing rule of atomic van der Waals parameters compared to AMBER/GAFF.

nakul20

Member

Registered: 2020-08-13

Posts: 6

Re: "Error encountered while loading atom in this file" - EDA-FF

Ah - that's true! Thanks for clarifying