how can i deal with this fatal error

srwjp001

Fatal error:
Syntax error - File h2o.itp, line 3
Last line read:
'[ moleculetype ]'
Invalid order for directive moleculetype

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I checked the list of .itp. in new files,
then the error changed

Fatal error:
Syntax error - File DEE_GMX.itp, line 3
Last line read:
'[ moleculetype ]'
Invalid order for directive moleculetype

[ atomtypes ] was inclued in top file

牧生

http://bbs.keinsci.com/thread-19320-1-1.html

srwjp001

牧生 发表于 2021-8-17 13:06
http://bbs.keinsci.com/thread-19320-1-1.html

thank you  for your reply. but the range has nothing different with sirsob

srwjp001

could you give me  more  details?

snljty

From sob's slides.

Common directives should follow this order when all included files in the top file are unfolded, especially any [ atomtypes ] should appear before all [ moleculetype ].

You forgot the [ atomtypes ] directive, e.g., [ atomtypes ]
;name   bond_type     mass     charge   ptype   sigma         epsilon       Amb
oh       oh          0.00000  0.00000   A     3.06647e-01   8.80314e-01 ; 1.72  0.2104
ho       ho          0.00000  0.00000   A     0.00000e+00   0.00000e+00 ; 0.00  0.0000

that should appear before your [ moleculetype ] directive.

Also, your [ molecules ] field is incorrect, the name should match exactly your name in [ moleculetype ], and nmols is the numer of molecules in your gro file, not the number of atoms. For your input file, it should be like:

[ molecules ]
; Compound        nmols
water              884   


Plus, your atom names in your top/itp files do not match your gro file. Those use lowercases are usually GAFF/GAFF2 types, which is used by acpype by default.

BTW, generally we seldom create topology file for water ourselves, since there are already bunches of expert water models that can be obtained from articles, e.g., SPC/E, OPC3, TIP4P-Ew, OPC, ...

srwjp001

snljty 发表于 2021-8-17 13:58
From sob's slides.

Common directives should follow this order when all included files in the top  ...

thank you for your kindness. i will check what you mentioned.: )