<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">In MD movie I loaded complex.prmtop and complex.inpcrd files<div class=""><br class=""></div><div class="">In Tools/Amber/Add ions I selected Ion types Na+ to neutralise complex.inpcrd using AMBER ff14SB for standard residues and AM1-BCC for other residues (I’m attaching a snapshot showing the Na+ ions in red).</div><div class=""><br class=""></div><div class="">I then proceeded to solvate the complex using TIP3PBOX and Box size: 9 </div><div class="">NOTE: I unticked the Removed existing ions/solvent box</div><div class=""><br class=""></div><div class="">I obtained the following Warning “Could not determine charges for pre-existing solvent/ions from added solvent/ions for: NA NA</div><div class=""><br class=""></div><div class="">I generated complex_solv.prmtop and complex_solv.inpcrd files</div><div class=""><br class=""></div><div class="">When I checked the complex_solv.prmtop file in cpptraj, I did not see any of the Na+ions (see below).</div><div class=""><div class=""><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(254, 244, 156);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">> resinfo</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(254, 244, 156);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">#Res Name First Last Natom #Orig #Mol</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(254, 244, 156);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""> 1 ASP 1 14 14 1 1 </span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(254, 244, 156);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""> 2 THR 15 28 14 2 1 </span> </div></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(254, 244, 156);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">———————</span></div><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(254, 244, 156);" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""> 250 LEU 3988 4006 19 250 3 </span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""> 251 VAL 4007 4023 17 251 3 </span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""> 252 KBR 4024 4062 39 252 4 </span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""> 253 WAT 4063 4065 3 253 5 </span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">————</span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">10272 WAT 34084 34086 3 10272 10024 </span></div><div style="margin: 0px; line-height: normal;" class=""><span style="font-variant-ligatures: no-common-ligatures;" class="">10273 WAT 34087 34089 3 10273 10025 </span></div><div class=""><span style="font-variant-ligatures: no-common-ligatures;" class=""><br class=""></span></div></span></div></span></div></div><div class=""><br class=""></div><div class="">Is this what should be expected? Should I consider the solvated complex charge neutralised?</div><div class=""><br class=""></div><div class="">Antechamber generated exactly the corresponding complex_solv.prmtop file with Na+ ions </div><div class=""><br class=""></div><div class="">Thank you in advance for any suggestions.</div><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-size: 11px; line-height: normal; font-family: Menlo; background-color: rgb(254, 244, 156);" class=""><img apple-inline="yes" id="A9AFE093-67A0-474B-A5D6-4899FE70DCC7" src="cid:B8611D46-83FE-4DBD-BBD7-503355B81AE3" class=""></div></div></body></html>