[gmx-users] Re: 3 covalent bonds protein- heme (malvezzi at iq.usp.br)

[Gerrit Groenhof]

You can use the specbond file:

and add entries like:

HID NE2 1 HEME FE 1 0.25 HID HEME

and run pdb2gmx with the -merge option.

Best

Gerrit

>
>   4. 3 covalent bonds protein- heme (malvezzi at iq.usp.br)
>   --------------
>
> Message: 4
> Date: Wed, 16 Sep 2009 18:40:16 -0300
> From: malvezzi at iq.usp.br
> Subject: [gmx-users] 3 covalent bonds protein- heme
> To: gmx-users at gromacs.org
> Message-ID: <20090916184016.7kfq1r9svcow4gwo at webmail.iq.usp.br>
> Content-Type: text/plain;	charset=ISO-8859-1;	DelSp="Yes";
> 	format="flowed"
>
> Dear Friends,
> I have to make three covalent bonds between the protein and the heme  
> group.
> I have parameters for heme and the residues.
> Do I have to make as if everything belongs to the same molecule?  (as
> it realy is)
> Has anyone done something like this?
> Thanks
> Alberto
>
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 17 Sep 2009 09:08:20 +0800
> From: Yang Ye <leafyoung at yahoo.com>
> Subject: Re: [gmx-users] compiling problem
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> 	<1b3c3eeb0909161808s2e01a4c9p3ce0a43646edc977 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Just a work-around, force mpicc to point to cc.
> alias mpicc=cc
>
> Yang Ye
>
> On Wed, Sep 16, 2009 at 5:35 PM, Mu Yuguang (Dr) <YGMu at ntu.edu.sg>  
> wrote:
>
>> No, even I do not use mpi , the error is still there.
>>
>>
>>
>> Regards
>>
>> Yuguang
>>
>>
>>  ------------------------------
>>
>> *From:* gmx-users-bounces at gromacs.org [mailto:
>> gmx-users-bounces at gromacs.org] *On Behalf Of *Yang Ye
>> *Sent:* Wednesday, September 16, 2009 2:34 PM
>> *To:* Discussion list for GROMACS users
>> *Subject:* Re: [gmx-users] compiling problem
>>
>>
>>
>> Is LAM-MPI's binary in PATH? if you run mpicc from console, will it  
>> also
>> show "No such file or directory"? Check LAM-MPI installation.
>>
>> Regards,
>> Yang Ye
>>
>> On Wed, Sep 16, 2009 at 12:39 PM, Mu Yuguang (Dr) <YGMu at ntu.edu.sg>  
>> wrote:
>>
>> Hi,
>> I use
>> git clone git://git.gromacs.org/gromacs.git
>>
>> to get the lastest version
>> and
>> ./bootstrap
>>
>> To generate the configure file
>> Then use ./configure successfully
>>
>> Howeve, after make
>> The error appears as foloowing:
>>
>>
>> mpicc -DHAVE_CONFIG_H -I. -I. -I../../../../src -I/usr/X11R6/include
>> -I/usr/include/libxml2 -I../../../../include
>> -DGMXLIBDIR=\"/home/ygmu/software/gmx_cvs/gromacs/share/top\"
>> -I/home/ygmu/software/fftw-3.2/float/include -O3 -fomit-frame-pointer
>> -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops - 
>> std=gnu99
>> -MT nb_kernel400_x86_64_sse.lo -MD -MP -MF .deps/ 
>> nb_kernel400_x86_64_sse.Tpo
>> -c nb_kernel400_x86_64_sse.c -o nb_kernel400_x86_64_sse.o
>> nb_kernel400_x86_64_sse.c: In function `nb_kernel400_x86_64_sse':
>> nb_kernel400_x86_64_sse.c:93: warning: implicit declaration of  
>> function
>> `_mm_castsi128_ps'
>> nb_kernel400_x86_64_sse.c:93: error: invalid initializer
>> nb_kernel400_x86_64_sse.c:94: error: invalid initializer
>> nb_kernel400_x86_64_sse.c:95: error: invalid initializer
>> mpicc: No such file or directory
>> make[5]: *** [nb_kernel400_x86_64_sse.lo] Error 1
>>
>> Regards
>>
>> Yuguang
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before  
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
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>>
>>
>>
>>
>> --
>> Regards,
>> Yang Ye
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before  
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
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>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
>
> -- 
> Regards,
> Yang Ye
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> End of gmx-users Digest, Vol 65, Issue 96
> *****************************************

--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://wwwuser.gwdg.de/~ggroenh/