leila karami wrote:
dear justin
I checked the VMD mailing list but that does not help me.
first few lines of my gro file :
Well, the structure of the .gro file appears intact. Somewhere along the way,
VMD thinks it's hitting the end of the file. Have you manipulated or edited the
file in any way? Opened it using some weird Windows software that saved some
hidden characters or something? If so, you can run it through dos2unix to
correct that.
As an aside, what kind of model are you using? You have explicit HA atoms on
the CA of GLY (OPLS? AMBER?), but no N-terminal protonation. That would seem to
be a completely fictitious and unreasonable model for a standard N-terminal
glycine. Not related to your problem, but I seem to be on a roll of free advice
this morning :)
-Justin
Protein in water
23136
1GLY N 1 1.655 4.898 3.866 -0.3222 -0.2420 0.1437
1GLY CA 2 1.677 4.774 3.793 0.0134 -0.2201 0.2050
1GLY HA1 3 1.579 4.735 3.767 0.5541 -1.5676 0.1443
1GLY HA2 4 1.732 4.708 3.859 1.2946 2.0442 1.5391
1GLY C 5 1.760 4.809 3.671 0.1350 -0.3085 0.2633
1GLY O 6 1.732 4.904 3.598 0.1431 -0.4147 0.1209
2SER N 7 1.867 4.733 3.644 0.3115 -0.0506 0.2274
2SER H 8 1.898 4.660 3.706 -1.4080 -0.0311 1.1663
2SER CA 9 1.924 4.738 3.511 -0.9271 0.2649 -0.3082
2SER HA 10 1.845 4.759 3.439 -0.6670 -0.9431 -0.9674
last few lines of my gro file :
7208Na Na23127 1.251 2.111 2.829 0.0512 -0.5390 0.2230
7209Na Na23128 0.220 2.894 0.285 -0.0656 0.2288 -0.0477
7210Na Na23129 2.803 0.503 5.080 0.0192 -0.1246 0.0370
7211Na Na23130 3.718 2.036 1.304 -0.4850 -0.3162 0.4396
7212Na Na23131 2.322 3.787 2.485 0.2661 0.1734 0.5773
7213Na Na23132 3.592 5.392 5.571 0.4515 0.6877 -0.3284
7214Na Na23133 4.708 2.478 0.651 -0.1105 0.1018 -0.4275
7215Na Na23134 4.612 4.964 0.340 0.2845 -0.3202 0.0326
7216Na Na23135 5.438 6.245 5.071 -0.0165 0.1414 -0.2011
7217Na Na23136 5.855 1.272 5.027 -0.3189 0.4687 -0.1455
6.21600 6.27700 6.26300
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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