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Dear Mark and other gmx users,<BR>
Thank you for the reply. In practice, I have a dendrimer in hand and find the two parts on two different neighbour residues have total charge 0. I think the two parts can be set as a charge group. My questions (1) and (2) become: is it reasonable to do so? Also to set all of them manually is not a trivial thing. My question (3) becomes: How to do so?<BR>
<BR>
Sincerely<BR>
Chaofu Wu<BR>
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wuxiao wrote:<BR>> Dear gmx users,<BR>> Recently, some questions puzzle me too much. While reading many <BR>> resources, I can not think out. Therefore, I would like to turn for this <BR>> mail-list. These questions are as follows:<BR>> (1) The total number of partial atom charge by summing the residue <BR>> must be zero? <BR> <BR>No, but it would usually be a good idea, lest some polymer end up with a<BR>non-zero charge.<BR> <BR>> (2) It can set several atoms into a charge group, which is neighbour <BR>> covalent but on different residues?<BR> <BR>It could, but in general this would prohibit use of pdb2gmx.<BR> <BR>> (3) There are some tools, which can help set the number of charge <BR>> group (cgnr£©?<BR> <BR>No. For example, they are coded in the .rtp file and pdb2gmx slavishly<BR>copies them.<BR> <BR>Mark<BR>
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