On 7/2/14, 5:39 AM, Linlin Sun wrote:
Hello everyone, In order to build a virtual site which is independent from other structure, I have created a new atom type and set the mass of this new atom type to zero. However, when I use* grompp*, it failed with fatal errors, which complain about the zero mass of the new atom type. Anyone could possibly know how to get around this problem? Any suggestions would be helpful. Thanks very much!
If you've declared it as an atom (particle type "A"), then that's probably why you're getting this error. Virtual site types are particle type "V" in ffnonbonded.itp. I guess the larger point is - why have a virtual site that is not dependent upon any other elements of the structure?
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