| 5:45:19 AM PST - Mon, Dec 18th 2017 |
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Hi everyone,
when I perform a QM/MM calculation for a protein with more than 2 peptide chains, I get the following error from the pre_short module:
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* 0: pre_shorts:increase dimension 2
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I removed all the non-standard residues from the pdb file already and successfully calculated a QM/MM energy with just the first one or two chains of the protein included. I also tried this for two other proteins with the same results. Thus, my pdb format seems to be fine, as well as my handling of the termination of one peptide chain (TER keyword).
I looked at the pre_short source code (https://svn.pnl.gov/svn/nwchem/trunk/src/prepar/pre_short.F), which lets me believe that this has something to do with searching for the smallest distance between some atoms (I don't know which atoms and what for). The error message arises from the line:
if(number.gt.10) call md_abort('pre_shorts:increase dimension',2)
Does someone know why this happens in my case and what this "number" variable does? How can I "increase the dimension", as it is suggested? It does not seem like this value 10 can be increased in any way. As I said, this problem only arises when my proteins starts having more than 2 separate chains.
Attaching my prepared pdb and input file somehow did not work. You can take a look at them here:
Just read input: https://pastebin.com/eeUdEy5g
Download pdb and input: https://files.fm/u/hcxxssqq#_
Hopefully someone can help me with this problem.
Best regards,
Cbru94
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