<div dir="ltr"><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><br><br> </div><div class="gmail_quote">On Fri, Jan 6, 2012 at 2:18 PM, Peter C. Lai <span dir="ltr"><<a href="mailto:pcl@uab.edu" target="_blank">pcl@uab.edu</a>></span> wrote:<br>
<blockquote style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid" class="gmail_quote">
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" value="+12012010612">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" value="+12012010612">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" value="+12012010601">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" value="+15402319080">(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>
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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" value="+16082626371">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" value="+12056900808">(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" value="+12056900808">(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" value="+17858645060">785-864-5060</a> Fax: <a href="tel:785-864-5396" target="_blank" value="+17858645396">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/~kuczera/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" value="+12056900808">(205) 690-0808</a> |<br>
==================================================================<br>
<br>
--<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br><div dir="ltr"><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>