Dear all,
I am planning to run a MD of a cytochrome using the NAMD Program. I have checked that topology files of CHARMM27 such as: (top_alll27_prot_lipid.inp) which includes some lines about the "heme group". However, when I try to run the Psfgen I got several errors. It seems that I need a patch for the conection of the Fe-Heme > group in my .tcl file. But I don´t really know where I could get this patch to include it in my .tcl file? Or If there is any other strategy to include the heme group in my MD simulation?
Thanks in advance and best regards
You can find the HEME residue's potential parameters in CHARMM force fields by a simple query.
Hello Ramin,
Thank you for your answer.
As I could remember, the heme residue's parameters were included in CHARMM27, however I got the error when running my .tcl file. Thus, seems that I must include something in such file (e.g patch, query) but I don't know how to do this.
Tcl scripts like other programing scripts are very sensitive to any term, so it's normal to face with some errors at your initial debuggings - try to be patient and find and solve them. If you faced with any specific errors that can not be solved please share. I had used HEME residue in a study to run a simulation in NAMD almost 15 years ago, I can not remember the details but please be sure that it can be done. TCL is a good baby and will let you know what needs along debugging.
Hello again Ramin. Thank you so much for your kind answer.
Yes, exactly. Tcl scripts are very sensitive. I have found one example of .tcl file used to run MD simulations with the Heme group (heme group text file). However I am not sure how to include some of this information in my .tcl file (citocromo2.tcl). Do you remember any detail on that?
Thanks in advance and best regards,
Marlet
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