Dear Mark<br><br>I generated the topology using pdb2gmx using dce.pdb. i checked the .top file and i contains necessary .itp files. the error message that i get is given below. any help is highly appreciated.<br><br>Program grompp, VERSION 4.0.7<br>
Source code file: toppush.c, line: 620<br><br>Fatal error:<br>Unknown bond_atomtype CLAA<br><br>Regards<br>Vinoth<br><br><br><div class="gmail_quote">On Mon, Oct 18, 2010 at 5:12 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div bgcolor="#ffffff" text="#000000"><div><div></div><div class="h5">
On 18/10/2010 10:31 PM, vinothkumar mohanakrishnan wrote:
<blockquote type="cite"> Hi all<br>
<br>
i added new atomtype for dichloroethane (DCE) and added the
corresponding parameters in the .rtp, .atp, .bon.itp, .nb.itp
respectively. given below are my additions to the corresponding
files respectively.<br>
<br>
<b>ffoplsaa.rtp</b><br>
<br>
[ DCE ]<br>
[ atoms ]<br>
CLAA opls_967 -0.2270 1<br>
CAB opls_966 0.2270 1<br>
CAC opls_966 0.2270 2<br>
CLAD opls_967 -0.2270 2<br>
<br>
[ bonds ]<br>
CLAA CAB<br>
CAB CAC<br>
CAC CLAD<br>
<br>
[ angles ]<br>
CLAA CAB CAC<br>
CAB CAC CLAD<br>
<br>
[ dihedrals ]<br>
CLAA CAB CAC CLAD<br>
<br>
<b>ffoplsaa.atp</b><br>
<br>
opls_966 14.02700 ; CH2 for DCE<br>
opls_967 35.45300 ; CL for DCE<br>
<br>
<b>ffoplsaabon.itp</b><br>
<br>
[bondtypes]<br>
CLAA CAB 1 0.17870 194137.6 ; CL-CH2 for DCE<br>
CAB CAC 1 0.15300 259408.0 ; CH2-CH2 for DCE<br>
CAC CLAD 1 0.17870 194137.6 ; CL-CH2 for DCE<br>
<br>
[angletypes]<br>
CLAA CAB CAC 1 108.200 368.192 ; C-C-CL for DCE<br>
CAB CAC CLAD 1 108.200 368.192 ; C-C-CL for DCE<br>
<br>
[dihedraltypes]<br>
CLAA CAB CAC CLAD 3 20.76096 -0.4184 27.011904
0.00000 0.00000 0.00000 ; for DCE<br>
<br>
<b>ffoplsaanb.itp</b><br>
<br>
opls_966 CAB 6 14.02700 0.227 A 3.98000e-01
4.76976e-01 ; CH2 of DCE<br>
opls_967 CLAA 17 35.45300 -0.227 A 3.16000e-01
0.20920e+01 ; Cl of DCE<br>
<br>
<b>dce.pdb</b><br>
<br>
HETATM 1 CLAA DCE 1 6.300 -2.280 1.360 1.00
20.00 CL<br>
HETATM 2 CAB DCE 1 5.060 -3.540 1.500 1.00
20.00 C<br>
HETATM 3 CAC DCE 1 4.320 -3.740 0.170 1.00
20.00 C<br>
HETATM 4 CLAD DCE 1 3.270 -2.350 -0.210 1.00
20.00 CL<br>
<br>
After adding all this, when i run grompp i get the error as <b>fatal
error Unknown bond_atomtype CLAA</b>. can any one tell me why
this happens?.<br>
</blockquote>
<br></div></div>
I can't tell until I know how you've invoked grompp, and how you
generated the .top file it needs, and which line of that .top grompp
doesn't like. When asking for help, please copy and paste all your
relevant commands, and any error messages in full, and any relevant
chunk of the .top. Check whether that .top file is #including the
correct .itp files.<br>
<br>
Mark<br>
</div>
<br>--<br>
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