Hi Justin<br><br>I corrected the mistake what you said and i am able to run energy minimisation and equilibration. but when i view my em.gro and equilibration.gro in VMD it seems to me that the bonds between the atoms are broken in molecules.I used g_energy to check weather the system has equilibrated to the required temperature (300K) i found that the variation in the temperature was 100K (plus r minus) . i am not able find out what went wrong. any help is highly appreciated.<br>
<br>Regards<br>Vinoth<br><br><div class="gmail_quote">On Mon, Oct 18, 2010 at 6:09 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</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 class="im"><br>
<br>
vinothkumar mohanakrishnan wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Justin<br>
<br>
what corrections i should make to ffoplsaan.itp to make it correct. what i should give instead of CAB and CLAA?.<br>
<br>
</blockquote>
<br></div>
You must use atom types, not names. Unfortunately, you've chosen to use atom names, which are also types, which makes all of this quite confusing if you're not sure what you're doing.<br>
<br>
You defined two new atom types - opls_966 (CAB) and opls_967 (CLAA), which are the only indicators you are allowed to use if introducing new types. Thus, references to atom names (CAC, CLAD) will generate fatal errors.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
i copied the .rtp .atp .itp files from usr/local/gromacs/share/gromacs/top to my working directory and added these parameters to the corresponding files. what you mean is should i need to add these parameters to the source directory ( usr/local/gromacs/share/gromacs/top)?<br>
<br>
</blockquote>
<br></div>
Your topology needs to be consistent with whatever files need to be included. By default, Gromacs checks the working directory first, but if you've moved to a new (sub)directory to carry out further steps, the grompp will not find your modified files, but will instead locate only the default force field files in $GMXLIB. Either keep all your work in one directory (which can get messy), or make use of the "include" keyword in the .mdp file. Any directory specified there will be searched after the working directory, but before $GMXLIB.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Regards<br>
Vinoth<div><div></div><div class="h5"><br>
<br>
On Mon, Oct 18, 2010 at 5:27 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
vinothkumar mohanakrishnan wrote:<br>
<br>
Hi all<br>
<br>
i added new atomtype for dichloroethane (DCE) and added the<br>
corresponding parameters in the .rtp, .atp, .bon.itp, .nb.itp<br>
respectively. given below are my additions to the corresponding<br>
files respectively.<br>
<br>
*ffoplsaa.rtp*<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>
*ffoplsaa.atp*<br>
<br>
opls_966 14.02700 ; CH2 for DCE<br>
opls_967 35.45300 ; CL for DCE<br>
<br>
*ffoplsaabon.itp*<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>
<br>
You shouldn't be using atom names in the [*types] directives. What<br>
you should be using are the interpolated types from ffoplsaanb.itp,<br>
thus you have only utilized opls_966 (CAB) and opls_967 (CLAA).<br>
<br>
*ffoplsaanb.itp*<br>
<br>
<br>
opls_966 CAB 6 14.02700 0.227 A 3.98000e-01<br>
4.76976e-01 ; CH2 of DCE<br>
opls_967 CLAA 17 35.45300 -0.227 A 3.16000e-01<br>
0.20920e+01 ; Cl of DCE<br>
<br>
*dce.pdb*<br>
<br>
HETATM 1 CLAA DCE 1 6.300 -2.280 1.360 1.00<br>
20.00 CL<br>
HETATM 2 CAB DCE 1 5.060 -3.540 1.500 1.00<br>
20.00 C<br>
HETATM 3 CAC DCE 1 4.320 -3.740 0.170 1.00<br>
20.00 C<br>
HETATM 4 CLAD DCE 1 3.270 -2.350 -0.210 1.00<br>
20.00 CL<br>
<br>
After adding all this, when i run grompp i get the error as<br>
*fatal error Unknown bond_atomtype CLAA*. can any one tell me<br>
why this happens?.<br>
<br>
<br>
Have you been sure to #include the correct (modified) force field<br>
files? That is, if you made a local copy and adjusted them, these<br>
won't be the files that pdb2gmx will #include by default.<br>
<br>
-Justin<br>
<br>
Regards<br>
Vinoth<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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