<div dir="ltr">According your help and "pdb2gmx -his -missing" I could create input files. Also I used grompp without error. However, for mdrun I got this error: <br><br><b>Function type CMAP Dih. not implemented in ip_pert</b><br>
<br>How can I figure it out?<br><br>Thanks,<br>Dariush<br><br><br><div class="gmail_quote">On Tue, Jan 10, 2012 at 4:37 PM, Krzysztof Kuczera <span dir="ltr"><<a href="mailto:kkuczera@ku.edu">kkuczera@ku.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 bgcolor="#FFFFFF" text="#000000">
Hi Dariush<br>
If you are using the CHARMM27 force field, then all topology and
parameters<br>
are in your share/top/charmm27.ff directory<br>
The defined molecules are listed in aminoacids.rtp and force field
parameters in <br>
numerous other files. CHARMM does not use 'HIS' for histidine, but
has HSD, HSE and HSP for the isomers with hydrogen at ND1, NE2 and
both.<br>
You can either set these isomers by hand - by editing your PDB file
or use the<br>
'pdb2gmx -his' option for interactive definition.<br>
<br>
The bonus of keeping 'HIS' names and interactive setup is that bonds
to heme<br>
iron will be generated based on the 'specbond.dat' entries, if HIS
NE2 nitrogens are close enough to the FE.<span class="HOEnZb"><font color="#888888"><br>
<br>
Krzysztof</font></span><div><div class="h5"><br>
<br>
<br>
On 1/10/12 2:40 PM, Dariush Mohammadyani wrote:
<blockquote type="cite">
<div>Does anybody know where can I find [ HIS ] parameters?<br>
<br>
Thanks,<br>
Dariush<br>
<br>
<br>
<div>On Sat, Jan 7, 2012 at 3:58 AM, Dariush Mohammadyani <span><<a href="mailto:d.mohammadyani@gmail.com" target="_blank">d.mohammadyani@gmail.com</a>></span>
wrote:<br>
<blockquote>
<div>
<div>Dear Peter and Krzyszto,</div>
<div> </div>
<div>Thank you. I am following your comments. If I get any
problem I will come back.</div>
<div>
<div>
<div> </div>
<div><br>
<br>
</div>
<div>On Fri, Jan 6, 2012 at 2:18 PM, Peter C. Lai <span><<a href="mailto:pcl@uab.edu" target="_blank">pcl@uab.edu</a>></span>
wrote:<br>
<blockquote>
He must be using an older version of Gromacs.
4.5.4 and lower don't have<br>
ACE in charmm27.<br>
<div>
<div><br>
On <a href="tel:2012-01-06%2012" target="_blank">2012-01-06 12</a>:59:56PM
-0600, Krzysztof Kuczera wrote:<br>
> Here is the blocking group from<br>
>
gromacs-4.5.5/share/top/charmm27.ff/aminoacids.rtp<br>
> KK<br>
><br>
> [ ACE ]<br>
> [ atoms ]<br>
> CH3 CT3 -0.270 0<br>
> HH31 HA 0.090 1<br>
> HH32 HA 0.090 2<br>
> HH33 HA 0.090 3<br>
> C C 0.510 4<br>
> O O -0.510 5<br>
> [ bonds ]<br>
> C CH3<br>
> C +N<br>
> CH3 HH31<br>
> CH3 HH32<br>
> CH3 HH33<br>
> O C<br>
> [ impropers ]<br>
> C CH3 +N O<br>
><br>
><br>
> On 1/6/12 12:40 PM, Peter C. Lai wrote:<br>
> > Corrected bonds section (sorry been
up all night)<br>
> ><br>
> > [ ACE ]<br>
> > [ atoms ]<br>
> > CH3 CT3 -0.27 0<br>
> > HH31 HA 0.09 1<br>
> > HH32 HA 0.09 2<br>
> > HH33 HA 0.09 3<br>
> > C C 0.51 4<br>
> > O O -0.51 5<br>
> > [ bonds ]<br>
> > CH3 HH31<br>
> > CH3 HH32<br>
> > CH3 HH33<br>
> > CH3 C<br>
> > C O<br>
> ><br>
> > Surprisingly, an .hdb entry for
ACE exists so you don't need to create one.<br>
> > (and the .hdb entry uses HH3 as the
base hydrogen name in ACE)<br>
> ><br>
> >><br>
> >> On <a href="tel:2012-01-06%2012" target="_blank">2012-01-06 12</a>:23:49PM
-0600, Peter C. Lai wrote:<br>
> >>> Gromos96 53A6 has it.<br>
> >>><br>
> >>> On <a href="tel:2012-01-06%2001" target="_blank">2012-01-06 01</a>:18:38PM
-0500, Dariush Mohammadyani wrote:<br>
> >>>> I tried charmm27 too.<br>
> >>>><br>
> >>>> Error:<br>
> >>>> Residue 'ACE' not found
in residue topology database<br>
> >>>><br>
> >>>> I tried all forcefield
in the list provided by "pdb2gmx", but non of
them<br>
> >>>> works.<br>
> >>>><br>
> >>>> Dariush<br>
> >>>><br>
> >>>><br>
> >>>> On Thu, Jan 5, 2012 at
1:42 PM, Robert Hamers<<a href="mailto:rjhamers@wisc.edu" target="_blank">rjhamers@wisc.edu</a>>
wrote:<br>
> >>>><br>
> >>>>> HEME is in the
charmm27 force field.<br>
> >>>>> bob h.<br>
> >>>>><br>
> >>>>><br>
> >>>>><br>
> >>>>><br>
> >>>>> On 1/5/2012 12:00
PM, Dariush Mohammadyani wrote:<br>
> >>>>><br>
> >>>>> Yes, I have PDB file
(1HRC.pdb). However, when I try to use
"pdb2gmx" I<br>
> >>>>> get this error:<br>
> >>>>><br>
> >>>>> Residue 'HEM' not
found in residue topology database<br>
> >>>>><br>
> >>>>> and HEM is Iron ion
inside this protein. I do not know which
forcefield is<br>
> >>>>> proper to use. I
also tried MARTINI force field according their
website; I<br>
> >>>>> used martinize.py
script; Again I got error.<br>
> >>>>><br>
> >>>>> Regards,<br>
> >>>>> Dariush<br>
> >>>>><br>
> >>>>><br>
> >>>>><br>
> >>>>><br>
> >>>>> On Thu, Jan 5, 2012
at 11:51 AM, Justin A. Lemkul<<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>
wrote:<br>
> >>>>><br>
> >>>>>><br>
> >>>>>> Dariush
Mohammadyani wrote:<br>
> >>>>>><br>
> >>>>>>> Hi all,<br>
> >>>>>>><br>
> >>>>>>> Has anybody
made initial configuration for Cytochrom C?
Can it be shared<br>
> >>>>>>> with me?<br>
> >>>>>>><br>
> >>>>>>><br>
> >>>>>> There are
several in the PDB.<br>
> >>>>>><br>
> >>>>>> -Justin<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>
> >>>>>> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a>
| <a href="tel:%28540%29%20231-9080" target="_blank">(540)
231-9080</a><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>
> >>>>>><br>
> >>>>>>
========================================<br>
> >>>>>><br>
> >>>>>> --<br>
> >>>>>> gmx-users
mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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> >>>>>><br>
> >>>>><br>
> >>>>><br>
> >>>>><br>
> >>>>><br>
> >>>>><br>
> >>>>><br>
> >>>>> --<br>
> >>>>> Robert J. Hamers<br>
> >>>>> Wisconsin
Distinguished Professor<br>
> >>>>> Univ. of
Wisconsin-Madison<br>
> >>>>> 1101 University
Avenue<br>
> >>>>> Madison, WI 53706<br>
> >>>>> Ph: <a href="tel:608-262-6371" target="_blank">608-262-6371</a><br>
> >>>>> Web: <a href="http://hamers.chem.wisc.edu" target="_blank">http://hamers.chem.wisc.edu</a><br>
> >>>>><br>
> >>>>><br>
> >>>><br>
> >>>> --<br>
> >>>> Kind Regards,<br>
> >>>> Dariush Mohammadyani<br>
> >>>> Department of Structural
Biology<br>
> >>>> University of Pittsburgh
School of Medicine<br>
> >>>> Biomedical Science Tower
3<br>
> >>>> 3501 Fifth Avenue<br>
> >>>> Pittsburgh, PA 15261<br>
> >>>> USA<br>
> >>>> --<br>
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> >>><br>
> >>> --<br>
> >>>
==================================================================<br>
> >>> Peter C. Lai
| University of Alabama-Birmingham<br>
> >>> Programmer/Analyst
| KAUL 752A<br>
> >>> Genetics, Div. of Research
| 705 South 20th Street<br>
> >>> <a href="mailto:pcl@uab.edu" target="_blank">pcl@uab.edu</a>
| Birmingham AL 35294-4461<br>
> >>> <a href="tel:%28205%29%20690-0808" target="_blank">(205)
690-0808</a> |<br>
> >>>
==================================================================<br>
> >>><br>
> >>> --<br>
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> >> --<br>
> >>
==================================================================<br>
> >> Peter C. Lai
| University of Alabama-Birmingham<br>
> >> Programmer/Analyst |
KAUL 752A<br>
> >> Genetics, Div. of Research | 705
South 20th Street<br>
> >> <a href="mailto:pcl@uab.edu" target="_blank">pcl@uab.edu</a>
| Birmingham AL
35294-4461<br>
> >> <a href="tel:%28205%29%20690-0808" target="_blank">(205)
690-0808</a> |<br>
> >>
==================================================================<br>
> >><br>
> >> --<br>
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><br>
><br>
> --<br>
> Krzysztof Kuczera<br>
> Professor<br>
> Departments of Chemistry and Molecular
Biosciences<br>
> The University of Kansas<br>
> 2010 Malott Hall<br>
> Lawrence, KS 66045<br>
> Tel: <a href="tel:785-864-5060" target="_blank">785-864-5060</a>
Fax: <a href="tel:785-864-5396" target="_blank">785-864-5396</a>
email: <a href="mailto:kkuczera@ku.edu" target="_blank">kkuczera@ku.edu</a><br>
> <a href="http://oolung.chem.ku.edu/%7Ekuczera/home.html" target="_blank">http://oolung.chem.ku.edu/~kuczera/home.html</a><br>
><br>
><br>
><br>
> --<br>
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<br>
--<br>
==================================================================<br>
Peter C. Lai | University
of Alabama-Birmingham<br>
Programmer/Analyst | KAUL 752A<br>
Genetics, Div. of Research | 705 South
20th Street<br>
<a href="mailto:pcl@uab.edu" target="_blank">pcl@uab.edu</a>
| Birmingham AL 35294-4461<br>
<a href="tel:%28205%29%20690-0808" target="_blank">(205)
690-0808</a> |<br>
==================================================================<br>
<br>
--<br>
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</div>
</div>
</blockquote>
</div>
<br>
<br>
<br>
-- <br>
<div>
<div>Kind Regards,<br>
Dariush Mohammadyani<br>
Department of Structural Biology<br>
University of Pittsburgh School of Medicine<br>
Biomedical Science Tower 3<br>
3501 Fifth Avenue<br>
Pittsburgh, PA 15261<br>
USA</div>
</div>
<br>
</div>
</div>
</div>
</blockquote>
</div>
<br>
<br>
<br>
-- <br>
<div>
<div>Kind Regards,<br>
Dariush Mohammadyani<br>
Department of Structural Biology<br>
University of Pittsburgh School of Medicine<br>
Biomedical Science Tower 3<br>
3501 Fifth Avenue<br>
Pittsburgh, PA 15261<br>
USA</div>
</div>
<br>
</div>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
<br>
<pre cols="72">--
Krzysztof Kuczera
Professor
Departments of Chemistry and Molecular Biosciences
The University of Kansas
2010 Malott Hall
Lawrence, KS 66045
Tel: <a href="tel:785-864-5060" value="+17858645060" target="_blank">785-864-5060</a> Fax: <a href="tel:785-864-5396" value="+17858645396" target="_blank">785-864-5396</a> email: <a href="mailto:kkuczera@ku.edu" target="_blank">kkuczera@ku.edu</a>
<a href="http://oolung.chem.ku.edu/%7Ekuczera/home.html" target="_blank">http://oolung.chem.ku.edu/~kuczera/home.html</a>
</pre>
</div></div></div>
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