Running QM/MM calculation by charmm on ubuntu 12.04
Clicked A Few Times
9:25:47 AM PST - Fri, Nov 30th 2012
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

                                 --------------



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://nwchemgit.github.io/Special_AWCforum/st/id602/Running_NWChem_in_parallel.ht...

thanks for your time



Varnon

Clicked A Few Times
9:29:29 AM PST - Mon, Dec 3rd 2012
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.

Clicked A Few Times
7:57:29 PM PDT - Thu, Jul 10th 2014
A SEGMENT FILE COULD NOT BE FOUND FOR spce
Quote:Varnon Dec 3rd 4:29 pm
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.

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.

Clicked A Few Times
7:43:56 AM PDT - Fri, Jul 11th 2014
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://nwchemgit.github.io/index.php/Release62:Getting_Started

Clicked A Few Times
2:35:50 AM PDT - Mon, Jul 14th 2014
is your .nwchemrc file well set?
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.

Clicked A Few Times
6:51:53 AM PDT - Mon, Jul 14th 2014
If you are using Ubuntu (or Linux in general I guess), you should prepare this file in your "home" directory.

Clicked A Few Times
7:05:16 PM PDT - Mon, Jul 14th 2014
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.

Clicked A Few Times
5:42:25 AM PDT - Tue, Jul 15th 2014
yes, this one..what is there inside?? is it pointing in the folder where you have the libraries and the .par files ?

Clicked A Few Times
6:34:18 PM PDT - Tue, Jul 15th 2014
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?

Clicked A Few Times
4:28:24 AM PDT - Wed, Jul 16th 2014
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..

Clicked A Few Times
7:06:40 PM PDT - Wed, Jul 16th 2014
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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