From NWChem
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| 8:25:47 AM PST - Fri, Nov 30th 2012 |
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Hello everyone,
I'm trying to run QM/MM calculation by charmm force field on Etl0.pdb example before to use this method on my work. But I have a problem during the task prepare. In particular when I run the job I receive an error:
Prepare QM/MM calculation of ethanol
------------------------------------
Prepare Module
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Force field charmm
Directories used for fragment and segment files
./
Parameter files used to resolve force field parameters
./charmm.par
PDB geometry etl0.pdb
Created segment ./etl.sgm
Created sequence ./etl.seq
A SEGMENT FILE COULD NOT BE FOUND FOR spce
**********
* 0: pre_dimens failed 9999
**********
If I try to comment the keyword charmm by # (so using amber FF) on my input file, the system works correctly.
My OS is ubuntu 12.04 LTS
and because I need to run in parallel I installed:
http://ftp.us.debian.org/debian/pool/main/n/nwchem/nwchem-data_6.1-4_all.deb
http://ftp.us.debian.org/debian/pool/main/n/nwchem/nwchem_6.1-4_amd64.deb
as suggested here:
http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id602/Running_NWChem_in_parallel.ht...
thanks for your time
Varnon
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| 8:29:29 AM PST - Mon, Dec 3rd 2012 |
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I resolved it by deletion of the word "0spce" in the *.seq file (only the word not the row). After this manage it is possible to run the job.
it is not necessary using Amber FF. I don't know why.
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| 6:57:29 PM PDT - Thu, Jul 10th 2014 |
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A SEGMENT FILE COULD NOT BE FOUND FOR spce
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Quote:Varnon Dec 3rd 4:29 pmI resolved it by deletion of the word "0spce" in the *.seq file (only the word not the row). After this manage it is possible to run the job.
it is not necessary using Amber FF. I don't know why.
hello varnon, I am new to nwchem. I have met the same error"A SEGMENT FILE COULD NOT BE FOUND FOR spce" during the task prepare. I delete the word "Ospe" in the *.seq file as you ,but I got the error:
Force field charmm
Directories used for fragment and segment files
./
Parameter files used to resolve force field parameters
./charmm.par
Deleted existing sequence ./MgSO4.seq
PDB geometry MgSO4.pdb
Created sequence ./MgSO4.seq
A SEGMENT FILE COULD NOT BE FOUND FOR spce
**********
* 0: pre_dimens failed 9999
**********
I know there must be something wrong with it, but I don't know how to do. I must admit that I'm a beginner in nwchem.
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| 6:43:56 AM PDT - Fri, Jul 11th 2014 |
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Hi Zll,
I'm not an expert since I'm also new in handling NWChem, btw, from you output, I can see that there is no information after "Directories used for fragment and segment files" and "Parameter files used to resolve force field parameters". So, my question is:
is your .nwchemrc file well set??
if not, you can find more info here:
http://www.nwchem-sw.org/index.php/Release62:Getting_Started
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| 1:35:50 AM PDT - Mon, Jul 14th 2014 |
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is your .nwchemrc file well set?
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| Pardon me, please.I have read the selection "Release62:Getting_Started". Whether the ".nwchemrc file" is about the installation or input files? I don't quite understand how to set my .nwchemrc file. Do you have some details? Pardon my ignorance again.
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| 5:51:53 AM PDT - Mon, Jul 14th 2014 |
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| If you are using Ubuntu (or Linux in general I guess), you should prepare this file in your "home" directory.
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| 6:05:16 PM PDT - Mon, Jul 14th 2014 |
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Do you mean the operation
"ln -s /usr/local/NWChem/data/default.nwchemrc $HOME/.nwchemrc"? If it is, I think I have. Or is something else going on? And yes, I am using Linux.
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| 4:42:25 AM PDT - Tue, Jul 15th 2014 |
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| yes, this one..what is there inside?? is it pointing in the folder where you have the libraries and the .par files ?
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| 5:34:18 PM PDT - Tue, Jul 15th 2014 |
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Oh,yes, the default.nwchemrc is following
nwchem_basis_library /public/software/nwchem/data/libraries/
nwchem_nwpw_library /public/software/nwchem/data/libraryps/
ffield amber
amber_1 /public/software/nwchem/data/amber_s/
amber_2 /public/software/nwchem/data/amber_q/
amber_3 /public/software/nwchem/data/amber_x/
amber_4 /public/software/nwchem/data/amber_u/
spce /public/software/nwchem/data/solvents/spce.rst
charmm_s /public/software/nwchem/data/charmm_s/
charmm_x /public/software/nwchem/data/charmm_x/
Any questions on that?
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| 3:28:24 AM PDT - Wed, Jul 16th 2014 |
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| if it point where you have the libraries, I don't know what it is going on...the only thing that I can say, it is that it looks like the code is not able to reach those libraries..
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| 6:06:40 PM PDT - Wed, Jul 16th 2014 |
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| Varnon, you make me realize the fact "I am a new learner" again. And yes, this is my first to contact nwchem. It is inevitable to do something wrong or forget something. Although I am reading the documentation carefully, I set some wrong parameters and necessary files. Could you send me some details and examples to let me improve or modify, please?
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