Juliette N. wrote:
Hi again,
I am wondering if using tpbconv to set zero charges (case 1) works
similar to when one sets zero atom charges in topology file from the
very beginning (case 2). Do these two cases work similarly?
They should work identically.
I checked tpr file and I see that charges are set to zero.
Can you please tell me what these lines mean?
Does it refer to exclusion which is set to 3 in top file?
Yes.
excls[0][0..10]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10}
excls[1][11..18]={0, 1, 2, 3, 4, 5, 6, 7}
The number of these lines corresponds to atom numbers in the system.
They refer to the atom indices of the atoms in the [moleculetype], not the
consecutive numbering of the system (for the first molecule this will be the
same, but I thought I'd point that out).
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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