VMD-L Mailing List

From: Stanley Lan (sclantw_at_hotmail.com)
Date: Fri Oct 28 2005 - 11:47:06 CDT

Hi Everyone,

When I work on the GROMOS demo molecule(PCL), I found that if I open the
attached file (lmmsxmd2.dat) in VMD and go to "Main Menu" -> "Graphics" ->
"Representation", then choose "Selections" tab -> and choose all but the
solvents which in the console the text is actually "all not not (protein or
sugar or nucleic or lipid)". I seemed lost the C-terminal residue (GLN)
along with all the waters. When I convert the gromos g96 format to pdb
format by using the program "gromos2dcd" written by Axel Kohlmeyer(By the
way, Thanks!), the pdb file(c9s3.pdb) gave me the same result (missing GLN).
  I am just wondering if anyone here had the similar problem. The
lmmmta1.dat file is the molecule topology file I used to run/generate the
problematic coordinates(lmmsxmd2.dat).

Best,
Stanley