On 6/12/13 12:10 AM, maggin wrote:
Hi, Justin,
You are right, I should first fix the bad geometry.
I check 1dx0.pdb, and the problematic areas are:
atom1 atom2
1 N1+ (GLY124 N) 4 H (GLY124 HT3)
181 C (PRO137 CD) 182 H (PRO137 HD1)
262 H (PHE141 HD1) 263 C (PHE141 CE2)
296 O1- (ASP144 OD2) 297 C (ASP144 C)
685 O (PRO165 O) 688 C (VAL166 CA)
for these atoms bonds that rotated more than 30 degrees
1dx0.pdb is get from NMR.
So, for the initial structure , is there anyways to solve these LINCS
WARNING ?
What does visual inspection tell you about these areas: (1) from the NMR
structure and (2) after steep minimization?
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* 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/Support/Mailing_Lists
