<div>Dear Gromacs users,</div> <div> </div> <div>Could you please help me to find out what the problem is.<BR>I use command<BR></div> <div>pdb2gmx -f C:\Soft\Gromacs\Input\formaldehyde.pdb -o outputName.gro -p outputName.top</div> <div> </div> <div>formaldehyde.pdb looks like this:<BR></div> <div>COMPND UNNAMED <BR>REMARK 1 PDB to MMOD atom-numbering translation table; the mmod numbers<BR>REMARK 1 pertain to the .dat file from which this file was created,<BR>REMARK 1 not to one created from this file:<BR>REMARK 1 PDB: 1
2 3 4 <BR>REMARK 1 MMOD: 1 2 3 4 /<BR>HETATM 1 C01 UNK 0 0.000 0.302 0.000 0.00 0.00 0<BR>HETATM 2 O02 UNK 0 0.000 1.510 0.000 0.00 0.00 0<BR>HETATM 3 H03 UNK 0 -0.960 -0.262 0.000 0.00 0.00 0<BR>HETATM 4 H04 UNK 0 0.960 -0.262 0.000 0.00 0.00 0<BR>CONECT 1 3
4<BR>CONECT 1 2<BR>CONECT 1 2<BR>CONECT 2 1<BR>CONECT 2 1<BR>CONECT 3 1<BR>CONECT 4 1<BR>END</div> <div> </div> <div>Gromacs output is</div> <div>-------------------------------------------------------<BR>Program pdb2gmx, VERSION <BR>Source code file: C:\Program Files\Microsoft Visual Studio\MyProjects\pdb2gmx\pdb2gmx\resall.cpp, line: 493</div> <div>Fatal error:<BR>Residue 'UNK' not found in residue topology database</div> <div>-------------------------------------------------------</div> <div>Thanx for Using GROMACS - Have a Nice Day</div> <div> </div> <div>Thank you in advance</div> <div> </div><p> 
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