I want to run MD simulation of my protein that is 479 a.a long. I found 6 bad contacts in my protein by the process mentioned in tutorial. http://ambermd.org/tutorials/advanced/tutorial8/loop5.htm
I want to know how can I set my input file for minimisation so that I may freeze my protein and only minimise water in order to remove bad contacts?
sample minimisation input is as given below:-
Minimization with Cartesian restraints for the solute &cntrl imin=1, maxcyc=200, ntpr=5, ntr=1, &end Group input for restrained atoms 100.0 RES 1 155 END END
Please suggest me how to add restraints for protein
Thank you
Hi Sadaf,
You should change "maxcyc=200" to "maxcyc=2000 ncyc = 1000" and "RES 1 155" to "RES 1 479".
http://ambermd.org/tutorials/basic/tutorial1/section5.htm
You have not used atom mask in your inpit file
pls use atom mask such as C CA N O
These tutorials may help.
https://ucanr.edu/sites/rizzolab/
You can use the following input file to restrain all protein atoms except for H, which shouldn't be restrained. All water molecules and counter-ions (if you have any) are allowed to relax. I also recommend increasing maxcyc to 2000 instead of 200, in addition to using ncyc flag, and to assigning a cutoff distance for non bonded interactions calculations.
Minimization with restraint on heavy atoms except water and hydrogen
&cntrl
imin=1,
irest=0, ntx=1,
maxcyc=2000, ncyc=100,
ntpr=50,
cut=10.0,
ntb=2, ntp=1,
ntr=1,
restraintmask= ‘! (@H=) &!(:WAT| @Na+=)’,
restraint_wt=50,
&end
END
END
Note 1: if you are using a counter-ion other than sodium, replace Na+ with your counter-ion. If you are not using any counter ions, just write the mask like this:
restraintmask= ‘! (@H=) &!(:WAT=)’,
Note 2: it is recommended to have a second minimization run where all restraints are removed so that you end up with a totally relaxed system.
thank you so much all of you
I will try these and if I get some problem will come back to you.@ Ravi singh here is no tutorial at the link you send me.
Ravi Singh can you please tell me how to mask
I am using amber for first time I dnt know how to use it
Sondos Musleh can you please tell me why we put restraint_wt=50. Means how can we calculate how much force to add.Also I am having following error when I use syntax as u gave me
Error in group input::atommask.f::selectElemMask
elementary mask does not start with : or @
Sadaf Rani
The "restraintmask" flag is used to specify the restrained atoms, while the "restraint_wt" flag specifies the weight (in kcal/mol.Å2) for the positional restraints. Stating it in a simpler way, it is how strongly you will hold the atoms restrained. The chosen value of 50 is due to personal preference. You can, however, use a weaker or a stronger restraint weight.
Sondos Musleh I am having following error when I use syntax as u gave me
Error in group input::atommask.f::selectElemMask
elementary mask does not start with : or @
Can you please suggest me how to correct it
Well, I've never encountered this error message before.
The problem could simply be due to an error in copying the text. I used to encounter many errors when I was copying the texts from the tutorials in the first few simulations I've run.
Try to write the text instead of copying it, or give me your email and I'll send you the input file and then use it directly.
I've used this input file to run too many simulations and all went smoothly. However, I'm using AMBER12, and I'm not sure whether this works with other versions or not. Anyway, give it another trial, and if it didn't work, then refer to AMBER and AMBER tools manuals for the version you are using.
Regarding the restraint weight used, well according to my supervisor, it doesn't really matter how much weight you use. I found 50 kcal/mol.Å2 reasonable and I've stuck to it.
Sondos Musleh Thank you so much for your suggestions
I put following
restraintmask= '(:* & !@H=) &!(@WAT | @Na+=)', and it worked for me. I am using amber 16 and amber tools 17.
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