<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>Hi gmx-users,<br><br>I have trying build topologies for PVC polymer in opls/aa forcefield. I read the chapter 5 and modified the files ffoplsaa.rtp, ffoplsaa.hdb, ffoplsaa-n.tdb, ffoplsaa-c.tdb, but not successful.<br>Below, you can see the blocks that built. The parameters for the residue may seem confusing, but I am trying to understand how to build these blocks and then create new parameters for the residue.<br><br>rtp file:<br><br>[ VIN ]<br> [ atoms ]<br> C1 opls_136 -0.120 1<br> H11 opls_140 0.060 1<br> H12 opls_140 0.060 1<br> C2
opls_001 0.500 2<br> Cl opls_151 -0.200 2<br> H21 opls_153 0.103 2<br> [ bonds ]<br> C1 H11<br> C1 H12<br> C1 C2<br> C2 Cl<br> C2 H21<br> C2 +C1<br><br>hdb file<br><br>VIN 2<br> 2 6 H1 C1 C2 +C1<br>
1 6 H2 C2 C1 -C2<br><br>-c.tdb file:<br><br>[ VIN ]<br> [ replace ]<br> C1 opls_135 12.011 -0.18<br> [ add ]<br> 3 4 H1 C1 C2<br> opls_140 1.008 0.06<br>[ delete ]<br> H21<br><br>-n.tdb file:<br><br>[ VIN ]<br>[ replace ]<br>C opls_152 12.011 -0.006<br>[ add ]<br>2
4 H C2 C1<br> opls_153 1.00800 0..103<br>[ delete ]<br> H21<br><br>By using the pdb2gmx following error occurs:<br><br>Opening library file ffoplsaa.rtp<br>Opening library file /usr/local/gromacs332/share/gromacs/top/aminoacids.dat<br>Reading PVC_32_mon_1_cd_gromos.pdb...<br>WARNING: all CONECT records are ignored<br>Read 194 atoms<br>Opening library file /usr/local/gromacs332/share/gromacs/top/xlateat.dat<br>26 out of 26 lines of xlateat.dat converted succesfully<br>Analyzing pdb file<br>There are 1 chains and 0 blocks of water and 32 residues with 194 atoms<br><br> chain #res #atoms<br> 1 ' ' 32 194<br><br>All occupancies are one<br>Opening library file
/usr/local/gromacs332/share/gromacs/top/ffoplsaa.atp<br>Atomtype 817<br>Reading residue database... (ffoplsaa)<br>Opening library file ffoplsaa.rtp<br>Residue 57<br>Sorting it all out...<br>Opening library file ffoplsaa.hdb<br>Opening library file ffoplsaa-n.tdb<br><br>-------------------------------------------------------<br>Program pdb2gmx_mpi, VERSION 3.3.2<br>Source code file: h_db.c, line: 95<br><br>Fatal error:<br>Error in hdb file ffoplsaa-n.tdb:<br>Wrong number of control atoms (2 iso 3) on line:<br>2 4 H C2 C1<br><br>Why this error occur?<br><br>Excuse me my English, I am a beginner in the language. <br><br> Thank you very much<br></div></div><br>
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