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rgb(0, 129, 194);}.textLink {cursor: pointer}</style><div id="tabMessageViewerBody_headeri60_611279037138895"><div id="2_messageHeaderDiv" class="messageHeaderDiv colorWhite fontT2
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fontHeadline" style="line-height: 20px;">Tue, July 13, 2010 11:46:58 AM</span><span id="2_messageHeaderFlag" class="headerControls"><div widget="" cmd="launch:toggle_flag" class="messageFlagIcon noflaggedIcon" style="margin-top: 3px;"></div></span></span><div id="2_messageHeaderSubject" class="ellip headerSubjectLine fontH1
fontDarkGray fontBold" style="width: 62%;"><div class="cgSelectable
ellip_text"><nobr style="width: 485px;" id="2_messageHeaderSubject_text" class="cgSelectable msgSubjText"><span widget="" cmd="msgaction_ext:subjectSearch" class="cgSelectable" style="cursor: pointer;" title="View all emails with this subject">grompp errors</span></nobr></div><span class="dots" id="2_messageHeaderSubject_dots">...</span></div></div></div><div class="posRel"><table class="fontT2 fontMedGray" cellpadding="0"><tbody><tr class="msgHeaderContainer"><td id="2_messageHeaderLabelCell"><nobr id="2_messageHeaderToLabel" class="headerRecipientLabel">From:</nobr></td><td><div id="2_messageHeaderSender" class="ellip headerSender" style="width: 245px;"><div class="cgSelectable ellip_text"><nobr id="2_messageHeaderSender_text" class="cgSelectable"><span widget="" cmd="msgaction_ext:senderSearch" class="cgSelectable" title="View all
emails from this sender "><span class="fontDarkGray">Amanda Watkins</span>
<mhstrumpetgirl@yahoo.com></span> <img id="_test_im_image_mhstrumpetgirl:0" class="onlineIcon" src="http://mail.yimg.com/a/i/us/pim/dclient/img/spacer_1.gif" style="position: relative; top: 1px; width: 12px; height: 12px; border: 0px none; cursor: pointer;" title="Chat now" onclick='top._cmd(
"im:open_im_session", null, null, "mhstrumpetgirl:0", "mailheader" )' onload="if(typeof throbberHack=='function')throbberHack();else if
(typeof parent.throbberHack=='function')parent.throbberHack();"></nobr></div><span class="dots" id="2_messageHeaderSender_dots">...</span></div><a id="2_messageHeaderABText" class="textLink msgHeaderLink fontT3
fontLink" cmd="msgaction_ext:viewContactDetails" widget="" title="View
Sender" s="" contact="" details="">View Contact</a></td></tr><tr id="2_messageHeaderToContainer" class="msgHeaderContainer"><td><nobr id="2_messageHeaderToLabel" class="headerRecipientLabel">To:</nobr></td><td><span class="cgSelectable">gmx-users@gromacs.org</span></td><td></td></tr></tbody></table></div></div><hr class="messageHeaderDivider colorK2" noshade="noshade"></div><div id="cg_msg_content"><style type="text/css"><!--DIV {margin:0px;}--></style><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div>Dear GROMACS users,<br><br>I am trying to simulate a protein
(OmpA) and a detergent (DPC) together in GROMACS. I have successfully
generate and minimized the protein and the detergent separately and now I
have inserted 216 DPC molecules into the protein box, and whenever I
try to upload them with grompp for mdrun, I get this message:<br><br>Ignoring
obsolete mdp entry 'title'<br>Ignoring obsolete mdp entry 'cpp'<br>Replacing
old mdp entry 'unconstrained_start' by 'continuation'<br><br>Back Off! I
just backed up mdout.mdp to ./#mdout.mdp.18#<br>checking input for
internal consistency...<br><br>NOTE 1 [file em.mdp, line unknown]:<br>
For energy conservation with switch/shift potentials, rlist should be
0.1<br> to 0.3 nm larger than rcoulomb.<br><br><br>NOTE 2 [file em.mdp,
line
unknown]:<br> For energy conservation with switch/shift potentials,
rlist should be 0.1<br> to 0.3 nm larger than rvdw.<br><br>processing
topology...<br>Opening library file /usr/share/gromacs/top/ffG53a6.itp<br>Opening
library file /usr/share/gromacs/top/ffG53a6nb.itp<br>Opening library
file /usr/share/gromacs/top/ffG53a6bon.itp<br>Opening library file
/usr/share/gromacs/top/ff_dum.itp<br>Generated 165 of the 1596
non-bonded parameter combinations<br>Opening library file
/usr/share/gromacs/top/spc.itp<br>Opening library file
/usr/share/gromacs/top/ions.itp<br>Excluding 3 bonded neighbours
molecule type 'Protein_A'<br>Excluding 3 bonded neighbours molecule type
'DPC'<br><br>NOTE 3 [file 1qjp.top, line 8723]:<br> System has
non-zero total charge: -1.000001e+00<br> <br><br><br>processing
coordinates...<br>double-checking input for internal consistency...<br>renumbering
atomtypes...<br>converting bonded parameters...<br><br>ERROR 1
[file 1qjp.top, line 8723]:<br> atom NC3 (Res DPC-1) has mass 0<br><br><br><br>ERROR
2 [file 1qjp.top, line 8723]:<br> atom PO4 (Res DPC-1) has mass 0<br><br><br><br>ERROR
3 [file 1qjp.top, line 8723]:<br> atom C1 (Res DPC-1) has mass 0<br><br><br><br>ERROR
4 [file 1qjp.top, line 8723]:<br> atom C2 (Res DPC-1) has mass 0<br><br><br><br>ERROR
5 [file 1qjp.top, line 8723]:<br> atom C3 (Res DPC-1) has mass 0<br><br><br><br>There
were 3 notes<br><br>-------------------------------------------------------<br>Program
grompp, VERSION 4.0.7<br>Source code file:
../../../../src/kernel/grompp.c, line: 986<br><br>Fatal error:<br>There
were 5 errors in input file(s)<br>-------------------------------------------------------<br><br>"Take
Your Medications and Preparations and Ram It Up Your Snout" (F. Zappa)<br><br><br>*Here is the file that it is having trouble processing:<br><br>dpc1.itp:<br><br>; topology for a dodecylphosphocholine
lipid<br> <br>[ moleculetype ]<br>; Name nrexcl<br>DPC 3<br><br>[
atoms ]<br>; nr type resnr residu atom cgnr
charge mass<br> 1 NL 1 DPC NC3
1 0.0 ; qtot: 2.24<br> 2 P 1 DPC
PO4 1 0.0 ; qtot: 3.28<br> 3
CH2 1 DPC C1 1 0.0 ; qtot: 1<br>
4 CH2 1 DPC C2 1 0.0 ; qtot: 1<br>
5 CH3 1 DPC C3 1 0.0 ; qtot: 3<br><br>Is there something that I am inputing wrong?
Or is it that I need to regenerate the DPC molecules to
include all of the atoms within the molecule? Whenever I tried to use the other .itp file it gives me the error that there is an atom difference. This new error is my attempt to fix this error.<br><br>Sincerely,<br><br>~Amanda
Watkins<br><br>SBC 2012<br></div>
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