[gmx-users] Need to confirm parameters.

Sailesh Bataju thelaven at gmail.com
Wed May 24 05:06:32 CEST 2017


>>* Making bonds...
*>>* Warning: Short Bond (5-1 = 0.0259999 nm)
*>>* Warning: Long Bond (5-6 = 0.99084 nm)
*>>* Warning: Long Bond (1-2 = 0.944378 nm)
*>>* Warning: Long Bond (1-3 = 0.895661 nm)
*>>* Warning: Long Bond (1-4 = 0.866986 nm)
*>>* Warning: Long Bond (7-8 = 0.502204 nm)
*>>* Warning: Long Bond (7-9 = 0.567317 nm)
*>> *Warning: Long Bond (7-10 = 0.92202 nm)
*>>* Warning: Long Bond (11-12 = 0.592831 nm)
*>>* Warning: Long Bond (11-13 = 0.700231 nm)
*>>* Warning: Long Bond (11-14 = 0.729592 nm)*

> The short bond warnings do, however, indicate that the starting geometry is bad.

> -Justin

I'd a doubt about it you eventually pointed it out sir, thank you.
Those bond lengths have drastic differences than the bond lengths
given in ffbonded.itp file. Here it goes according to the .itp file:-

1-5 = 0.15380000 nm

5-6 = 0.11110000 nm

1-2 = 0.11110000 nm

and so on...

Nothing has matched with those generated bonds. It looks like I've to
modify pdb file manually for correct geometry using distance formula
or is there some other way to do it, sir?

Thank you very much.


More information about the gromacs.org_gmx-users mailing list