From NWChem
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Just Got Here
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| 6:26:19 PM PDT - Tue, Oct 9th 2012 |
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I thought I'd get my feet wet with NWChem by running a simple geometry optimization on citrate, however I find that I run into problems loading the initial coordinates from a pdb using the latest version (6.1.1) with MPI. Here is my very basic script: start GeomOpt
memory total 24000 mb
echo
charge -3
geometry units angstrom
load cit.pdb
end
basis
* library 6-31G*
end
title "Hartree-Fock Optimization"
task scf optimize
Which inevitably results in:
NWChem Input Module
-------------------
------------------------------------------------------------------------
reading coordinates geom_read_file_pdb 0
------------------------------------------------------------------------
input error at line 9: at end of line looking for character string
load cit.pdb
------------------------------------------------------------------------
current input line :
9: load cit.pdb
------------------------------------------------------------------------
------------------------------------------------------------------------
This error has not yet been assigned to a category
------------------------------------------------------------------------
For more information see the NWChem manual at http://www.nwchem-sw.org/index.php/NWChem_Documentation
For further details see manual section: No section for this category
0:0:reading coordinates geom_read_file_pdb:: 0
(rank:0 hostname:jaguar pid:8138):ARMCI DASSERT fail. ../../ga-5-1/armci/src/common/armci.c:ARMCI_Error():208 cond:0
Now when I generate a xyz file (save the pdb as a xyz file in VMD), and try to load that instead, everything proceeds normally, but I'd really like to know why my initial approach didn't work. After the first failure, I stripped the PDB of everything but the required ATOM and END lines to no avail. 
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Marat Forum:Admin, Forum:Mod, NWChemDeveloper, bureaucrat, sysop
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Clicked A Few Times
Threads 2
Posts 43
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| 2:49:14 PM PDT - Thu, Oct 11th 2012 |
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If you post your pdb file I can take a look at it.
Marat
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