Celia González Moya

4 Questions 1 Answers 0 Followers

Questions related from Celia González Moya

What is the best way to parameterize a novel residue for Xplor-NIH?

I want to obtain the NMR structure of a synthetic peptide using Xplor-NIH. The compound has a residue that does not appear in the FF of the Xplor-NIH and I am interested in parametrizing it....

10 October 2018 1,804 1 View

Why when I try to refine the structure of a peptide with Xplor-NIH the following error occurs?

annealtt.py(48): protocol.genExtendedStructure() fixupCovalentGeom: Covalent geometry still violated at exit. ........ As a result, some angles and dihedrals are violated, and structures are not...

09 September 2018 8,597 0 View

Why LTOD patch, deform the structure of aromatics rings...?

I'm building a psf for Xplor, I use LTOD patch to change L-proline to D in a peptide, but when I visualize the structure in VMD, the rings of PHE and TYR deform...That is absurd, because the patch...

04 April 2018 8,301 0 View

During an MD simulation the disulfide bonds are increasing over time, can someone help us with this?

We are doing a molecular dynamic simulation with GROMACS using the AMBER force field. During the simulation the disulfide bonds are increasing over time. We set the bridge manually with pdb2gmx...

06 June 2015 5,691 3 View