Hi JiYuan,
My apologies for the slow response time.
On 4/01/2012, at 3:07 AM, JiYuan Liu wrote:
> I used the command "antechamber -i ca.out -fi gout -o ca.prepin -fo prepi -c resp -s 2 *-nc -2*" to rebuild ca.prepin of my ligand,I used another command "prep2xml" to build the new calib.xml for my ligand,at this moment I encountered a new small problem that it represented excessed symbol 	 in the lines of the new calib.xml.I have attached the log and output files after performed "prep2xml",Please have a look for them.
I haven't seen this problem before. It looks as though it may be a text encoding issue. Do you know what text encoding you were using at the time you prepared your input? Martin may be able to advise better on this, but I suspect MCPB probably works best with ASCII or UTF-8 encoded text.
> Although I found the small problem in the above,I just delete the symbol "	" in the calib.xml and replaced the old calib.xml.Everything looked fine when I performed "sh run.MCPB.csh",I found no difference at 3H68_OH_sidechain_opt.com and 3H68_OH_large_mk.com as before I used the old wrong calib.xml,so I didn't recalculate the Side Chain Model Optimization/Frequency Calculation and Large Model Charge Calculation.
Good. I'm pleased that you could save time in that way.
> Then I performed 5000 steps minimization and 10ps molecule dynamics,the small molecule,two ZN2+ ions,and the around amino acids which coordinates two ZN2+ were so stable.I need your help to give me a judge whether my this solution is reasonable.
We can't really offer a parameter validation service. Ultimately, you'll need to be the judge. Do the parameters seem reasonable in themselves? When you simulate with them, do the results make physical and chemical sense?
Best,
Ben
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jan 12 2012 - 06:00:03 PST
