Re: [cellulose-builder: 14] argument : monolayer

[Thiago Gomes]

Dear Ahmad, thank you for using our code and reporting your questions/problems. 

Please edit file `input.inp` to control which cellulose allomorph to build (default is I-beta).

Allomorphs supported are: cellulose I-beta, cellulose II, cellulose I-alpha, cellulose III_I (three subscript one).

There is no beta-II cristalline fase, just cellulose II.

For monolayers from cellulose allomorphs I-beta and II choose either `center` or `origin` as first argument.

For allomorph I-alpha monolayers type `monolayer` as first argument. 

Cellulose I-beta has two types of cellulose chains, center and origin, see http://pubs.acs.org/doi/abs/10.1021/ja0257319 .

Cellulose I-alpha has just one type of chain.

Best Regards,

Thiago

2012/10/30 Ahmad Rafsanjani <ahmad.ra...@gmail.com>

Thank you for sharing this nice code.

 

I have one problem and one question:

 

Problem: the argument monolayer does not work while all others work properly!

Question: how can we distinguish between beta-I and beta-II ? Does origin refers to beta-I and center to beta-II?

 

 

Best regards

 

Ahmad Rafsanjani

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[xueweijiang]

Dear Dr.,

Thank you for sharing this nice code.

I have a question with using cellulose builder, can you help me? I want to do some molecular dynamics by using AMBER. However, the atom types  and  sequence are not suit to AMBER. I have converted the pdb into the type suited to the leap of AMBER by the method, which combined the Cartesian coordinate of pdb provided by this program with the atom types and atom sequence defined by AMBER(force field GLYCAM_06).  Is this method right? If wrong, how can I convert the pdb file into the AMBER file type prmtop?

 

Best regards

Xuewei Jiang