Re: [SIESTA-L] Designing of protein structure

Dear Younas, I reckon you need to find a template (not temple), for example searching collagen in Protein Data Bank. Or even you do a litereature survey and find out a crystal structure of collagen. With the initial crystal, you then do modifications that you want. Cheers! Jin On 19/03/20

Re: [SIESTA-L] Designing of protein structure

Dear Younas, I reckon you need to find a temple, for example searching collagen in Protein Data Bank. Or even you do a litereature survey and find out a crystal structure of collagen. With the initial crystal, you then do modifications that you want. Cheers! Jin On 19/03/2015 3:38 AM, You

Re: [SIESTA-L] SIESTA Compilation problem

Let me also note that if you succeed in compiling you should do so without COMP_LIBS=dc_lapack.a I believe the divide and conquer algorithm is present in your used version of MKL. If you get compiler errors you can re-add the flag. 2015-03-18 21:41 GMT+00:00 Nick Papior Andersen : > Try this (f

Re: [SIESTA-L] SIESTA Compilation problem

Try this (from the main trunk directory): cd Src/MPI patch mpi_siesta.f90 mpi_siesta.patch cd ../../Obj rm -rf MPI ../Src/obj_setup.sh then try and make again, please respond whether it works :) 2015-03-18 19:36 GMT+00:00 Szendrő Márton : > My arch.make file has fall behind, I've attached it t

[SIESTA-L] SIESTA Compilation problem

Hi all, I'm trying to compile siesta-trunk-462 on a HPC cluster for paralell running. The cluster consists of AMD Opteron 6174 cpu-s. I'm using MKL, OpenMPI, Scalapack, NETCDF libraries. I got the following error during compilation: ==> Incorporating information about present compilation (compile

Re: [SIESTA-L] SIESTA Compilation problem

My arch.make file has fall behind, I've attached it this time 2015-03-18 20:34 GMT+01:00 Szendrő Márton : > Hi all, > > I'm trying to compile siesta-trunk-462 on a HPC cluster for paralell > running. The cluster consists of AMD Opteron 6174 cpu-s. I'm using MKL, > OpenMPI, Scalapack, NETCDF libra

[SIESTA-L] LDA+U

Dear Siesta users and developers, Is the LDA+U version only for serial execution? Anyone has successfully done parallel calculations? Best, Xiaoming Wang Postdoc Rutgers

Re: [SIESTA-L] Designing of protein structure

Thanks jin but how should I design the structure, lets say in pdb or xyz format?? On Wed, Mar 18, 2015 at 4:25 PM, Jingxian Yu wrote: > Dear Younas, > > I quote the following paragraph from wikipedia ( > http://en.wikipedia.org/wiki/Collagen). > > "Collagen is composed of a triple helix, which

Re: [SIESTA-L] Designing of protein structure

Dear Younas, I quote the following paragraph from wikipedia (http://en.wikipedia.org/wiki/Collagen). "Collagen is composed of a triple helix, which generally consists of two identical chains (α1) and an additional chain that differs slightly in its chemical composition (α2).^[27]

Re: [SIESTA-L] Designing of protein structure

Dear Jingxian Yu, Actually I am working on collagen protein which has a long tiple helix structure but I would like to have at least one tripeptide from each of the three chains of collagen triple helix. The tripeptide should most probably be GLY-PRO-HYP. Regards On Wed, Mar 18, 2015 at 3:48 PM,

Re: [SIESTA-L] Designing of protein structure

Dear Younas, Sorry your question is not clear to me! Do you mean the "protein" is a tripeptide, or quite long but only contains three types of amino acids? I have been working with peptide design and synthesis for some time. I hope I could help you if your question is clearer. Cheers! Jin

[SIESTA-L] [***Posible SPAM***]Re: Designing of protein structure

hi I guess you should check the protein data bank website for a pdb file nearest to your protein structure. and then use vmd to extract the cofactors /peptide chains/amino acid fragments from the protein for our protein, and export it to smaller pdb/xyz files. the fragments in turn can be manipulat

[SIESTA-L] Designing of protein structure

Hi all. I want to design a protein structure from three amino acids. Unfortunately I am unable to find the structure of required protein or its constituent amino acids in materials studio. How can I design the structure? kindly help me. thanks Younas Khan