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#29997 - 05/15/12 09:45 PM Charmm General Force Field (CGenFF) for a ligand
huyue Offline
Forum Member

Registered: 05/14/12
Posts: 2

I using CGENFF & the https://www.paramchem.org/ website to found a ligand . After generate psf file ,when run the nve equilibration ,it comes the errors .

MDIO: illegal value: no parameters exist for dihedral cg331 cg311 cg331 hga3

But I have merge the parameter file , CGENFF parameter file , the CHarmm 27 parameter file && the parameter file form that website.


Expect to your reply~

Best ~

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#29998 - 05/16/12 12:30 AM Re: Charmm General Force Field (CGenFF) for a ligand [Re: huyue]
wang Offline
Forum Member

Registered: 09/22/08
Posts: 6
Hi huyue,
The error message shouldn't appear if the parameter files are merged correctly. Note that all the parameter files have an 'END' tag at the very end of the file, and simply 'cat' all files into one will not work if your program ignores whatever that comes after the END tag. If you feel that you've done the merging correctly and the error persists, it will help others to decipher the error if you could provide more info.

Best,
Yi

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#30000 - 05/16/12 09:34 AM Re: Charmm General Force Field (CGenFF) for a ligand [Re: wang]
huyue Offline
Forum Member

Registered: 05/14/12
Posts: 2
thanks your reply


I using inpmerge software (http://nova.colombo58.unimi.it/manual/utilities/inpmerge.htm )to complete my target .

And I merge that 3 parameter files.

My ligand is IPTG (http://en.wikipedia.org/wiki/Isopropyl_%CE%B2-D-1-thiogalactopyranoside )a small ligand .

It comes that many dihedral angle is missing .

Best.

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#30002 - 05/16/12 11:38 AM Re: Charmm General Force Field (CGenFF) for a ligand [Re: huyue]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4302
Loc: ~ 59N, 15E
Perhaps you should ask your question to the "inpmerge" support then?
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#30003 - 05/16/12 11:40 AM Re: Charmm General Force Field (CGenFF) for a ligand [Re: huyue]
lennart Offline

Forum Member

Registered: 09/25/03
Posts: 4302
Loc: ~ 59N, 15E
This question seems to be posted at the wrong site. CHARMM does not issue any "MDIO" message.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#30335 - 07/06/12 05:46 PM Re: Charmm General Force Field (CGenFF) for a ligand [Re: huyue]
Kenno Online   content
Forum Member

Registered: 12/19/05
Posts: 1493
Loc: Baltimore, MD
Sorry for my very late reply; this post is mainly for future reference.

We do to some extent support using the CHARMM force field with other programs, so as long as users adhere to the local forum guidelines and stay on-topic ("parameter set"), I personally feel it's legitimate to ask questions about other programs in this forum.

The particular issue user "huyue" brought up has been asked to me several times before, so I decided to dedicate a new FAQ entry to it.

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