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 (malve...@iq.usp.br)
--------------
Message: 4
Date: Wed, 16 Sep 2009 18:40:16 -0300
From: malve...@iq.usp.br
Subject: [gmx-users] 3 covalent bonds protein- heme
To: gmx-users@gromacs.org
Message-ID: <20090916184016.7kfq1r9svcow4...@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 <leafyo...@yahoo.com>
Subject: Re: [gmx-users] compiling problem
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID:
<1b3c3eeb0909161808s2e01a4c9p3ce0a43646edc...@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) <y...@ntu.edu.sg>
wrote:
No, even I do not use mpi , the error is still there.
Regards
Yuguang
------------------------------
*From:* gmx-users-boun...@gromacs.org [mailto:
gmx-users-boun...@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) <y...@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
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Regards,
Yang Ye
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Regards,
Yang Ye
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*****************************************
--
Gerrit Groenhof
MPI biophysical chemistry
Goettingen
Germany
http://wwwuser.gwdg.de/~ggroenh/
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