From: 李文娟 (wenjuanli_at_sjtu.edu.cn)
Date: Thu Jun 23 2016 - 03:28:47 CDT
Dear NAMD users,
I am currently using VMDs NetworkView plugin for the analysis of the biosimulations carried out in AMBER .I have encountered some problems regrading the construction of covariance matrix prior to Networks calculations.Here is error message:
clusterSelString: residue ……
……
<prepareNodeMap
can't read "nodeMap(1341)": no such element in array
We can see from adjacency.psf ,the error occurred around the phosphorylated T165.
1340 A 165 TPO CB CT1 0.140000 12.0110 0
1341 A 165 TPO O5' ON2 -0.660000 15.9994 0
1342 A 165 TPO P PL 1.500000 30.9740 0
And I find a residue is added automatically next T165(the loggy.log file numbered residue from 0):
clusterSelString: residue 164 and name N CA CB O5' P O1P O2P OT CG2 C O
1337 1338 1339 1340 1345 1346 1347
clusterSelString: residue 166 and name N CA CB CG CD1 CE1 CZ CD2 CE2 C O
1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358
I think the error is due to the PSF file I created,especially phosphorylation site.But I dont know wht I should do.I will very appreciate if anyone can offer some suggestions.
Look forward to your reply!
Best wishes.
wjli
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