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标题: how can i deal with this fatal error [打印本页]

作者
Author: srwjp001 时间: 2021-8-17 13:00
标题: how can i deal with this fatal error
本帖最后由 srwjp001 于 2021-8-18 11:58 编辑

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

作者
Author: 牧生 时间: 2021-8-17 13:06
http://bbs.keinsci.com/thread-19320-1-1.html

作者
Author: srwjp001 时间: 2021-8-17 13:18

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

作者
Author: srwjp001 时间: 2021-8-17 13:24
could you give me more details?

作者
Author: snljty 时间: 2021-8-17 13:58
本帖最后由 snljty 于 2021-8-17 22:16 编辑

From sob's slides.
(, 下载次数 Times of downloads: 11)
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, ...

作者
Author: srwjp001 时间: 2021-8-17 16:42

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.: )

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