Hi pawan ,<br><br> Thanks for your right suggestion bu t after editing lipid.itp the another error comes like this-<br> <br>processing topology...<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx.itp<br>
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxnb.itp<br>Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxbon.itp<br>Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp<br>Generated 1369 of the 2211 non-bonded parameter combinations<br>
Opening library file /usr/local/gromacs/share/gromacs/top/flexspc.itp<br>Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp<br>Excluding 3 bonded neighbours molecule type 'DMPC'<br>Excluding 2 bonded neighbours molecule type 'SOL'<br>
processing coordinates...<br>Warning: atom name 1 in dmpc.top and dmpc-box.pdb does not match (CN1 - C1)<br>Warning: atom name 2 in dmpc.top and dmpc-box.pdb does not match (CN2 - C2)<br>Warning: atom name 3 in dmpc.top and dmpc-box.pdb does not match (CN3 - C3)<br>
Warning: atom name 4 in dmpc.top and dmpc-box.pdb does not match (NTM - N4)<br>Warning: atom name 5 in dmpc.top and dmpc-box.pdb does not match (CA - C5)<br>Warning: atom name 6 in dmpc.top and dmpc-box.pdb does not match (CB - C6)<br>
Warning: atom name 7 in dmpc.top and dmpc-box.pdb does not match (OA - O7)<br>Warning: atom name 8 in dmpc.top and dmpc-box.pdb does not match (P - P8)<br>Warning: atom name 9 in dmpc.top and dmpc-box.pdb does not match (OB - O9)<br>
Warning: atom name 10 in dmpc.top and dmpc-box.pdb does not match (OC - O10)<br>Warning: atom name 11 in dmpc.top and dmpc-box.pdb does not match (OD - O11)<br>Warning: atom name 12 in dmpc.top and dmpc-box.pdb does not match (CC - C12)<br>
Warning: atom name 13 in dmpc.top and dmpc-box.pdb does not match (CD - C13)<br>Warning: atom name 14 in dmpc.top and dmpc-box.pdb does not match (OE - O14)<br>Warning: atom name 15 in dmpc.top and dmpc-box.pdb does not match (C2A - C15)<br>
Warning: atom name 16 in dmpc.top and dmpc-box.pdb does not match (OF - O16)<br>Warning: atom name 17 in dmpc.top and dmpc-box.pdb does not match (C2B - C17)<br>Warning: atom name 18 in dmpc.top and dmpc-box.pdb does not match (C2C - C18)<br>
Warning: atom name 19 in dmpc.top and dmpc-box.pdb does not match (C2D - C19)<br>Warning: atom name 20 in dmpc.top and dmpc-box.pdb does not match (C2E - C20)<br>(more than 20 non-matching atom names)<br><br>WARNING 1 [file dmpc.top, line 20]:<br>
5888 non-matching atom names<br> atom names from dmpc.top will be used<br> atom names from dmpc-box.pdb will be ignored<br>double-checking input for internal consistency...<br>renumbering atomtypes...<br>converting bonded parameters...<br>
initialising group options...<br>processing index file...<br>Analysing residue names:<br>Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat<br>There are: 3783 OTHER residues<br>There are: 0 PROTEIN residues<br>
There are: 0 DNA residues<br>Analysing Other...<br>Making dummy/rest group for T-Coupling containing 16853 elements<br>Making dummy/rest group for Acceleration containing 16853 elements<br>Making dummy/rest group for Freeze containing 16853 elements<br>
Making dummy/rest group for Energy Mon. containing 16853 elements<br>Making dummy/rest group for VCM containing 16853 elements<br>Number of degrees of freedom in T-Coupling group rest is 50556.00<br>Making dummy/rest group for User1 containing 16853 elements<br>
Making dummy/rest group for User2 containing 16853 elements<br>Making dummy/rest group for XTC containing 16853 elements<br>Making dummy/rest group for Or. Res. Fit containing 16853 elements<br>Making dummy/rest group for QMMM containing 16853 elements<br>
T-Coupling has 1 element(s): rest<br>Energy Mon. has 1 element(s): rest<br>Acceleration has 1 element(s): rest<br>Freeze has 1 element(s): rest<br>User1 has 1 element(s): rest<br>User2 has 1 element(s): rest<br>
VCM has 1 element(s): rest<br>XTC has 1 element(s): rest<br>Or. Res. Fit has 1 element(s): rest<br>QMMM has 1 element(s): rest<br>Checking consistency between energy and charge groups...<br>
<br>NOTE 1 [file em.mdp, line unknown]:<br> You are using a plain Coulomb cut-off, this will often produce artifacts.<br> You might want to consider using PME electrostatics.<br><br><br>This run will generate roughly 2 Mb of data<br>
writing run input file...<br><br>There was 1 note<br><br>There was 1 warning<br><br>-------------------------------------------------------<br>Program grompp, VERSION 4.0.3<br>Source code file: gmx_fatal.c, line: 481<br><br>
Fatal error:<br>Too many warnings (1), grompp terminated.<br>If you are sure all warnings are harmless, use the -maxwarn option.<br>-----------------------------------------------------<br>If u know the solution of this problem please let me know.<br>
<br><br>Thanks in advance.<br><br>Nitu Sharma<br>School of life sciences<br>Jawaherlal Nehru University<br>New Delhi India<br>