[gmx-users] missing atoms

[ninoo mani]

Dear gmx users

 

I have a protein molecule with few missing residues,

a Lys with CG, CD, CE, NZ missing atoms, and

a Val with CG1, CG2 missing atoms.

I noticed that pdb2gmx reads the pdb file and places the missing atoms.

First I want to know whether gromacs places only missing atoms or it places the entire side chain?

Second, is gromacs' repaired molecule reliable for simulation or I should do homology modelling using other softwares to repair the molecule?

Thanks,

Ninoo

---

Here’s a new way to find what you're looking for - Yahoo! Answers

_______________________________________________
gmx-users mailing list    gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php