Jessé Nóbrega wrote:
Hi gmx-users,
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.
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.
rtp file:
[ VIN ]
[ atoms ]
C1 opls_136 -0.120 1
H11 opls_140 0.060 1
H12 opls_140 0.060 1
C2 opls_001 0.500 2
Cl opls_151 -0.200 2
H21 opls_153 0.103 2
[ bonds ]
C1 H11
C1 H12
C1 C2
C2 Cl
C2 H21
C2 +C1
hdb file
VIN 2
2 6 H1 C1 C2 +C1
1 6 H2 C2 C1 -C2
-c.tdb file:
[ VIN ]
[ replace ]
C1 opls_135 12.011 -0.18
[ add ]
3 4 H1 C1 C2
opls_140 1.008 0.06
[ delete ]
H21
-n.tdb file:
[ VIN ]
[ replace ]
C opls_152 12.011 -0.006
[ add ]
2 4 H C2 C1
opls_153 1.00800 0..103
[ delete ]
H21
By using the pdb2gmx following error occurs:
Opening library file ffoplsaa.rtp
Opening library file /usr/local/gromacs332/share/gromacs/top/aminoacids.dat
Reading PVC_32_mon_1_cd_gromos.pdb...
WARNING: all CONECT records are ignored
Read 194 atoms
Opening library file /usr/local/gromacs332/share/gromacs/top/xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 32 residues with 194 atoms
chain #res #atoms
1 ' ' 32 194
All occupancies are one
Opening library file /usr/local/gromacs332/share/gromacs/top/ffoplsaa.atp
Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
Residue 57
Sorting it all out...
Opening library file ffoplsaa.hdb
Opening library file ffoplsaa-n.tdb
-------------------------------------------------------
Program pdb2gmx_mpi, VERSION 3.3.2
Source code file: h_db.c, line: 95
Fatal error:
Error in hdb file ffoplsaa-n.tdb:
Wrong number of control atoms (2 iso 3) on line:
2 4 H C2 C1
Why this error occur?
You need three control atoms; you only have two (2 iso 3 means "2 instead of
3"). Refer to the manual for the proper syntax for these entries.
You may find this post helpful:
http://www.gromacs.org/pipermail/gmx-users/2009-March/040125.html
It refers to building a polyethylene polymer topology, but I think some of the
information should be generally applicable.
Also, don't bother with -n.tdb and -c.tdb files. If pdb2gmx does not detect
protein, I think these files are ignored. At least, it seems that way based on
others' difficulties.
-Justin
Excuse me my English, I am a beginner in the language.
Thank you very much
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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