<DIV>Dear gmxers,<BR> Yesterday, I posted a mail titled "pdb2gmx stop at "AtomType 1" " where I mentioned that I used gmx-4.5.1. The resulting problem is again posted below. Today, I turn to the gmx-4.0.7, and use the same pdb and rtp files with the name modified to compatible to the version. Strangely, it is found that the pdb2gmx of this version can generate the top file without any errors. Could you give me clues to why the latest version can not whereas the older version can? To get the clear help, my pdb and rtp files are also posted below. Thanks a lot for any reply.</DIV>
<DIV>Chaofu Wu, Dr.</DIV>
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<DIV>My command line and the screen output:<BR><A href="mailto:xiaowu759@linux-s38y:~/workshop">xiaowu759@linux-s38y:~/workshop</A>> pdb2gmx -f deta.pdb -o deta.gro -p deta.top -i deta.itp -ter<BR> :-) G R O M A C S (-:<BR> Gromacs Runs One Microsecond At Cannonball Speeds<BR> :-) VERSION 4.5.1 (-:<BR>......<BR>Opening force field file oplsaa.ff/aminoacids.r2b<BR>Reading deta.pdb...<BR>Read 20 atoms<BR>Analyzing pdb file<BR>Splitting PDB chains based on TER records or changing chain id.<BR>There are 1 chains and 0 blocks of water and 1 residues with 20 atoms<BR> chain #res #atoms<BR> 1 ' ' 1 20 <BR>All occupancies are one<BR>Opening force field file oplsaa.ff/atomtypes.atp<BR>Atomtype 1</DIV>
<DIV><BR>My pdb file:<BR>ATOM 1 N1 MOL 1 -5.199 1.343 0.334 1.00 0.00 N <BR>ATOM 2 C2 MOL 1 -4.582 0.639 1.470 1.00 0.00 C <BR>ATOM 3 C3 MOL 1 -3.897 1.462 2.593 1.00 0.00 C <BR>ATOM 4 N4 MOL 1 -3.194 0.615 3.574 1.00 0.00 N <BR>ATOM 5 C5 MOL 1 -2.373 1.331 4.566 1.00 0.00 C <BR>ATOM 6 C6 MOL 1 -1.520 0.397 5.464 1.00 0.00 C <BR>ATOM 7 N7 MOL 1 -0.684 1.133 6.432 1.00 0.00 N <BR>ATOM 8 H12 MOL 1 -4.614 2.067 -0.035 1.00 0.00 H <BR>ATOM 9 H11 MOL 1 -6.128 1.694 0.483 1.00 0.00 H <BR>ATOM 10 H22 MOL 1 -3.826 -0.053 1.056 1.00 0.00 H <BR>ATOM 11 H21 MOL 1 -5.345 -0.016 1.926 1.00 0.00 H <BR>ATOM 12 H31 MOL 1 -4.628 2.144 3.065 1.00 0.00 H <BR>ATOM 13 H32 MOL 1 -3.141 2.116 2.124 1.00 0.00 H <BR>ATOM 14 H41 MOL 1 -3.854 0.018 4.043 1.00 0.00 H <BR>ATOM 15 H51 MOL 1 -2.980 2.003 5.204 1.00 0.00 H <BR>ATOM 16 H52 MOL 1 -1.679 1.992 4.016 1.00 0.00 H <BR>ATOM 17 H62 MOL 1 -0.857 -0.180 4.795 1.00 0.00 H <BR>ATOM 18 H61 MOL 1 -2.188 -0.346 5.939 1.00 0.00 H <BR>ATOM 19 H72 MOL 1 -0.023 0.541 6.916 1.00 0.00 H <BR>ATOM 20 H71 MOL 1 -1.253 1.554 7.143 1.00 0.00 H <BR>TER</DIV>
<DIV>My rtp file:<BR>[ DET ]<BR> [ atoms ]<BR> N1 opls_900 -0.900 1<BR> H11 opls_909 0.360 1<BR> H12 opls_909 0.360 1<BR> C2 opls_906 0.060 1<BR> H21 opls_911 0.060 1<BR> H22 opls_911 0.060 1<BR> C3 opls_907 0.080 2<BR> H31 opls_911 0.060 2<BR> H32 opls_911 0.060 2<BR> N4 opls_901 -0.780 2<BR> H41 opls_910 0.380 2<BR> C5 opls_907 0.080 2<BR> H51 opls_911 0.060 2<BR> H52 opls_911 0.060 2<BR> C6 opls_906 0.060 3<BR> H61 opls_911 0.060 3<BR> H62 opls_911 0.060 3<BR> N7 opls_900 -0.900 3<BR> H71 opls_909 0.360 3<BR> H72 opls_909 0.360 3<BR> [ bonds ]<BR> N1 H11<BR> N1 H12<BR> N1 C2<BR> C2 H21<BR> C2 H22<BR> C2 C3<BR> C3 H31<BR> C3 H32<BR> C3 N4<BR> N4 H41<BR> N4 C5<BR> C5 H51<BR> C5 H52<BR> C5 C6<BR> C6 H61<BR> C6 H62<BR> C6 N7<BR> N7 H71<BR> N7 H72<BR></DIV>
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