All atom elastic network models

[Xinqiu Yao]

We have repeatedly received requests for ENMs that consider sidechains. See related issue #250. This feature is still under development in the branch feature-aanma, but should be included in next release. Currently, the function 'aanma()' supports following force fields:

• inverse power of six distance dependent (parameters to be optimized)
• Tirion-like distance cutoff based

and will include more force fields in future such as:

• the beta-GM model [Micheletti et al., Proteins 2004]
• ...

Also, we need an associated aanma.pdbs() for ensemble NMA.

Comments are welcomed!

[leleonp]

Hi, When I use aanma.pdbs i get the next error

Error in load.enmff("aaenm2") : force field not defined

I see in this post that are 2 ff available, however, i don't know how load them. Any advice will be helpfull. Thanks in advance

[Lars Skjærven]

Did you install the latest version of the feature_aanma branch? If so load.enmff("aaenm2") should be available.

[leleonp]

I load the aanma.pdbs function directly in R. Clearly is not the rigth way

[Lars Skjærven]

then you need to load all associated functions. I would recommend you to do the following:

install.packages("devtools")
library(devtools)
install_bitbucket("Grantlab/bio3d", subdir = "ver_devel/bio3d/", ref="feature_aanma")
library(bio3d)

good luck!

[leleonp]

Thanks!! Best regards

[leleonp]

The ff problema has been solved, but now i have the next error

Error in (function (pdb, pfc.fun = NULL, mass = TRUE, temp = 300, keep = NULL,  : 
Could not find the function " .nma.args "

Thanks

[Lars Skjærven]

are you sure you got the version installed properly? try to restart R and make sure you have bio3d_2.2-3.9000 loaded using sessionInfo

> library(bio3d)
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Workstation release 6.7 (Santiago)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] bio3d_2.2-3.9000

[leleonp]

After restart R works perfectly. Thanks again Best regards