Search found 6 matches

by vas2201
2018.09.21 22:05
Forum: Mixtures and Flexible Systems
Topic: Error : Gajoe : Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Replies: 1
Views: 5324

Error : Gajoe : Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Hello, I am getting the following error, while using gajoe module on extrenal pool, could you please sugget me needful to fix this bug ! [srp106@hpc4 aMD-2.1]$ gajoe -p < gajoe.in ******* ------------------------------------------------------ ******* ******* GAJOE - version 2.1 - (r7883) ******* ***...
by vas2201
2018.09.13 00:45
Forum: Mixtures and Flexible Systems
Topic: Gajoe run on external pool
Replies: 0
Views: 9970

Gajoe run on external pool

I am trying to run gajoe module on pool from MD simulation using shell script, I am getting the following error. But if ran it the terminal command ( gajoe -p ), it was working fine. . I want to give the default parameters as input file and running gajoe -p < input file. I am getting segmentation fa...
by vas2201
2018.08.28 20:39
Forum: Mixtures and Flexible Systems
Topic: onefile script
Replies: 17
Views: 17646

Re: onefile script

Hey alex,

Could you please send the one file script to penumutchu.srinivas@gmail.com.

Thank you !
by vas2201
2018.08.28 20:31
Forum: Mixtures and Flexible Systems
Topic: Reg : Gajoe run an external pool (own pool) results negative chi2 Value
Replies: 0
Views: 10260

Reg : Gajoe run an external pool (own pool) results negative chi2 Value

Hello, I am running GAJOE on the external pool that I created from amber MD trajectory! I used VMD script to write the PDB files. I ran the Gajoe -p to select the conformational ensemble which agrees with SAX data. Looks like GAJOE run was fine. but the log file was showing negative chi2 value and i...
by vas2201
2018.08.16 18:46
Forum: Mixtures and Flexible Systems
Topic: Reg : EOM structures and RDC refinement
Replies: 2
Views: 4902

Re: Reg : EOM structures and RDC refinement

Dear Hayds, Thanks for your reply! yes! I mean that global orientation of the domains is the orientation of the domains relative to each other in each model. can we obtain the relative domain orientation from EOM structures or at least can we use those structures (the subset of structures which have...
by vas2201
2018.08.14 00:00
Forum: Mixtures and Flexible Systems
Topic: Reg : EOM structures and RDC refinement
Replies: 2
Views: 4902

Reg : EOM structures and RDC refinement

Dear ATSAS users, We are currently working on flexible protein (HNRNP proteins ), consist of two domains with the flexible linker. We would like to use EOM generated structures as starting structures for further RDC refinement using amber MD protocols. When we ran the EOM, it generated mainly three ...