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<DIV>Hi, </DIV>
<DIV>I am trying to run MD for protein-lipid complex. I included in topology
file "protein.itp", "ffgmx.itp", "lipid.itp", "dmpc.itp". </DIV>
<DIV>When I run preprocessing </DIV>
<DIV>grompp -f em.mdp -c pro_lip.gro -p pro_lip.top -o pro_lip.tpr -maxwarn 1000
grompp gives some warnings like :</DIV>
<DIV><BR>WARNING 1 [file "C:/gromacs/share/top/ffgmx.itp", line 6]:<BR>
Found another defaults entry, will use the last one<BR>WARNING 2 [file
"C:/gromacs/share/top/ffgmxnb.itp", line 3]:<BR> Overriding atomtype
O<BR>WARNING 3 [file "C:/gromacs/share/top/ffgmxnb.itp", line 4]:<BR>
Overriding atomtype OM<BR>WARNING 4 [file "C:/gromacs/share/top/ffgmxnb.itp",
line 5]:<BR> Overriding atomtype OA<BR>WARNING 5 [file
"C:/gromacs/share/top/ffgmxnb.itp", line 9]:<BR> Overriding atomtype
OW<BR>WARNING 6 [file "C:/gromacs/share/top/ffgmxnb.itp", line 11]:<BR>
Overriding atomtype N<BR>WARNING 7 [file "C:/gromacs/share/top/ffgmxnb.itp",
line 12]:<BR> Overriding atomtype NT<BR>WARNING 8 [file
"C:/gromacs/share/top/ffgmxnb.itp", line 13]:<BR> Overriding atomtype
NL<BR>WARNING 9 [file "C:/gromacs/share/top/ffgmxnb.itp", line 14]:<BR>
Overriding atomtype NR5<BR>WARNING 10 [file "C:/gromacs/share/top/ffgmxnb.itp",
line 15]:<BR> Overriding atomtype NR5*<BR>WARNING 11 [file
"C:/gromacs/share/top/ffgmxnb.itp", line 16]:<BR> Overriding atomtype
NP<BR>WARNING 12 [file "C:/gromacs/share/top/ffgmxnb.itp", line 17]:<BR>
Overriding atomtype C<BR>WARNING 13 [file "C:/gromacs/share/top/ffgmxnb.itp",
line 18]:<BR> Overriding atomtype CH1<BR>WARNING 14 [file
"C:/gromacs/share/top/ffgmxnb.itp", line 19]:<BR> Overriding atomtype
CH2<BR>WARNING 15 [file "C:/gromacs/share/top/ffgmxnb.itp", line 20]:</DIV>
<DIV>.</DIV>
<DIV>.</DIV>
<DIV>.</DIV>
<DIV><FONT face=Arial size=2>WARNING 54.....</FONT></DIV>
<DIV><FONT face=Arial size=2>...</FONT></DIV>
<DIV>processing coordinates...<BR>Warning: atom names in pro_lip.top and
pro_lip.gro don't match (CN1 - CA)<BR>Warning: atom names in pro_lip.top and
pro_lip.gro don't match (CN2 - CB)<BR>Warning: atom names in pro_lip.top and
pro_lip.gro don't match (CN3 - CC)<BR>Warning: atom names in pro_lip.top and
pro_lip.gro don't match (NTM - N)<BR>Warning: atom names in pro_lip.top and
pro_lip.gro don't match (CA - CD)<BR>Warning: atom names in pro_lip.top and
pro_lip.gro don't match (CB - CE)<BR>Warning: atom names in pro_lip.top and
pro_lip.gro don't match (CC - CF)<BR>Warning: atom names in pro_lip.top and
pro_lip.gro don't match (CD - CG)<BR>Warning: atom names in pro_lip.top and
pro_lip.gro don't match (CE - CH)<BR>WARNING 55 [file "pro_lip.top", line
20]:<BR> 9 non-matching atom names<BR> atom names from pro_lip.top
will be used<BR> atom names from pro_lip.gro will be ingnored</DIV>
<DIV> </DIV>
<DIV><FONT face=Arial size=2>---------------------------------</FONT></DIV>
<DIV>Could anybody tell me, what these warnings means ?</DIV>
<DIV> </DIV>
<DIV>Thanks in advance</DIV>
<DIV> </DIV>
<DIV>Eva<BR><BR></DIV>
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