Dear AMBER
During my data analysis, I had two problems with ptraj and couldn't overcome them.
1- Snapshot extracting: when I extracted a snapshot from my MD simulation, I got a structure half of my protein is out of the water box, I have done refit and image options.
****
trajin Step1.mdcrd
trajin Step2.mdcrd
trajin Step3.mdcrd
trajin Step4.mdcrd
center :1-223
mass origine
image origin center
trajout Combined.mdcrd
*****
2- Average structure:
I had a 2ns simulation length partitioned on 4 mdcrd files. I combined these 4 mdcrd files and centered it using ptraj. I wanted to get the average strututre of the simulation. I got a structure with some groups cross-linked. These groups are free rotated groups e.g. CH3 group. is that right? or I made something wrong? How can I solve this problem in order to use the average structure for QM/MM optimization.
Here is my ptraj command:
trajin Step1.mdcrd
trajin Step2.mdcrd
trajin Step3.mdcrd
trajin Step4.mdcrd
center :1-223
mass origine
image origin center
trajout Combined.mdcrd
***********
trajin Combined.mdcrd
strip :WAT
average average_structure.pdb pdb
**********
Any kind of help would be highly appreciated
Thanks in advance
W. Flak
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Received on Thu Aug 26 2010 - 17:30:03 PDT
