<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><DIV>Hello,</DIV>
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<DIV> I am attempting to see if I can process and run a hydroxide ion using the ffG43a1 force field. In doing this I have read through chapter 5 of the manual and have a couple of questions. I do realize that the chemistry and physics of this will need to be justified, but at this point I'm just trying to make sure my thought process is right with regards to topology processing by GROMACs.</DIV>
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<DIV>1) I am first looking to approximate the atomtype by using the OW and H designated atoms names from ffG43a1.atp.</DIV>
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<DIV>2) Next ,with regards to residue type, I am looking to designate a new residue [-OH] in the ffG43a1.rtp files. My real question comes here. For example, for [HOH] format, </DIV>
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<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><B style="mso-bidi-font-weight: normal"><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt"><FONT size=1>[ HOH ]<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></FONT></SPAN></B></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt"><FONT size=1><STRONG><SPAN style="mso-spacerun: yes"> </SPAN>[ atoms ]<o:p></o:p></STRONG></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt"><FONT size=1><SPAN style="mso-spacerun: yes"> </SPAN>OW<SPAN style="mso-spacerun: yes"> </SPAN>OW<SPAN style="mso-spacerun: yes"> </SPAN>-0.82000<SPAN style="mso-spacerun: yes"> </SPAN>0<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt"><FONT size=1><SPAN style="mso-spacerun: yes"> </SPAN>HW1<SPAN style="mso-spacerun: yes"> </SPAN>H<SPAN style="mso-spacerun: yes"> </SPAN>0.41000<SPAN style="mso-spacerun: yes"> </SPAN>0<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt"><FONT size=1><SPAN style="mso-spacerun: yes"> </SPAN>HW2<SPAN style="mso-spacerun: yes"> </SPAN>H<SPAN style="mso-spacerun: yes"> </SPAN>0.41000<SPAN style="mso-spacerun: yes"> </SPAN>0<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt"><FONT size=1><STRONG><SPAN style="mso-spacerun: yes"> </SPAN>[ bonds ]<o:p></o:p></STRONG></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt"><FONT size=1><SPAN style="mso-spacerun: yes"> </SPAN>OW<SPAN style="mso-spacerun: yes"> </SPAN>HW1<SPAN style="mso-spacerun: yes"> </SPAN>gb_35<SPAN style="mso-spacerun: yes"> </SPAN><o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt"><FONT size=1><SPAN style="mso-spacerun: yes"> </SPAN>OW<SPAN style="mso-spacerun: yes"> </SPAN>HW2<SPAN style="mso-spacerun: yes"> </SPAN>gb_35<SPAN style="mso-spacerun: yes"> </SPAN><o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt"><FONT size=1><SPAN style="mso-spacerun: yes"> </SPAN>HW1<SPAN style="mso-spacerun: yes"> </SPAN>HW2<SPAN style="mso-spacerun: yes"> </SPAN>gb_41<SPAN style="mso-spacerun: yes"> </SPAN><o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt"><FONT size=1><SPAN style="mso-spacerun: yes"> </SPAN><STRONG>[ angles ]<o:p></o:p></STRONG></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt"><FONT size=1>;<SPAN style="mso-spacerun: yes"> </SPAN>ai<SPAN style="mso-spacerun: yes"> </SPAN>aj<SPAN style="mso-spacerun: yes"> </SPAN>ak<SPAN style="mso-spacerun: yes"> </SPAN>gromos type<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><FONT size=1><STRONG><SPAN style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt"><SPAN style="mso-spacerun: yes"> </SPAN></SPAN><SPAN lang=IT style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt; mso-ansi-language: IT">[ impropers ]<o:p></o:p></SPAN></STRONG></FONT></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN lang=IT style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt; mso-ansi-language: IT"><FONT size=1>;<SPAN style="mso-spacerun: yes"> </SPAN>ai<SPAN style="mso-spacerun: yes"> </SPAN>aj<SPAN style="mso-spacerun: yes"> </SPAN>ak<SPAN style="mso-spacerun: yes"> </SPAN>al<SPAN style="mso-spacerun: yes"> </SPAN>gromos type<o:p></o:p></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN lang=IT style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt; mso-ansi-language: IT"><FONT size=1><STRONG><SPAN style="mso-spacerun: yes"> </SPAN>[ dihedrals ]<o:p></o:p></STRONG></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN lang=IT style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt; mso-ansi-language: IT"><FONT size=1>;<SPAN style="mso-spacerun: yes"> </SPAN>ai <SPAN style="mso-spacerun: yes"> </SPAN>aj<SPAN style="mso-spacerun: yes"> </SPAN>ak<SPAN style="mso-spacerun: yes"> </SPAN>al<SPAN style="mso-spacerun: yes"> </SPAN>gromos type</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN lang=IT style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt; mso-ansi-language: IT"><FONT size=1></FONT></SPAN> </P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN lang=IT style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt; mso-ansi-language: IT"><FONT size=3>I understand how I would designate the atoms and bonds, but do I have to bother with the angles, impropers and dihedrals subsections as shown since I have a diatomic entity? If yes, I assume GROMACs will know I have a diatomic and obviously not attempt to assign any of these values?</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN lang=IT style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt; mso-ansi-language: IT"><FONT size=3></FONT></SPAN> </P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN lang=IT style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt; mso-ansi-language: IT"><FONT size=3>Last, if I designate this hydroxide and it works, will this prevent pdb2gmx from automatically assigning a proton to my hydroxide(thus making water)? This is important as I am looking to observe hydroxide behavior as an anionic ligand to ZN2+Any guidance you could provide would be appreciated.</FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN lang=IT style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt; mso-ansi-language: IT"><FONT size=3></FONT></SPAN> </P>
<P class=MsoNormal style="MARGIN: 0in 0in 0pt"><SPAN lang=IT style="FONT-SIZE: 10pt; mso-bidi-font-size: 12.0pt; mso-ansi-language: IT"><FONT size=3>Thanks, Marc</FONT></SPAN></P>
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