Use Moltemplate gaff.lt Cant built

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1

Hello.

I try make molecular by moltemplate.

Display sucu under error message.

-----error message-----

No bond types defined for the bond between
atoms /atom:NaSSs[2][2][2]/O3 (type @/atom:GAFF/o) and /atom:NaSSs[2][2][2]/Na1 (type @/atom:GAFF/na)

-----end-----

Please tell me,Do i do what?

2

Hello Murai

I am not certain the reason for your error. Usually this occurs if the user made a mistake in the atom type. But in your case, I can not see where the mistake is.

Can you send me your .lt files?

Thanks

Andrew

---- details ----

In the “Bonds By Type” section of the “gaff.lt” file, I see that there are 3 possible ways of binding a sodium atom (@atom:na) to an oxygen atom:

write_once(“Data Bonds By Type”) {

:
@bond:na-o @atom:na @atom:o
@bond:na-oh @atom:na @atom:oh
@bond:na-os @atom:na @atom:os
:
}

(lines 1582-1584)

This suggests to me that your oxygen atom should be one of these types
(@atom:GAFF/o @atom:GAFF/oh or @atom:GAFF/os)

After looking at the error message you got, I realize you did use one of these atom types (@atom:GAFF/o). Consequently, this could indicate there might be a bug somewhere.

Anyway, please send me your input files.

Cheers

3

You probably didn't define that bond

Check out: http://lammps.sandia.gov/doc/bond_style.html

Respectfully,
Mohammad Athar

4

You probably didn't define that bond

Check out: http://lammps.sandia.gov/doc/bond_style.html

I don't think so.
This is an error message generated by moltemplate.sh, not LAMMPS, so
the problem is moltemplate-specific. Moltemplate is supposed to
choose the bond-types according to the atom-types. At first glance at
"gaff.lt", it appears as though a bond-type was assigned to this pair
of atom types.

    Even if there is no bug in "moltemplate.sh" or "gaff.lt", I would
like to find out how to make it easier for users to avoid these kinds
of errors, so I'm curious to know what happened. But I need a
complete list of .LT files ("system.lt", etc...) in order to reproduce
the error.

Andrew

P.S. If you don't want to share your molecular secrets, feel free to
modify your files. Just make sure they generate the same error
message. Also, simplifying the LT sometimes makes the debugging
easier.