[Dock-fans] GCC 4.3 and compiling Dock 6.2 errors

[Prism Sciences]

Dr. Stone,
   Yes, I was successful in installing on both a Gentoo 2008.0 system  
and Ubuntu 8.10.  but to do so, I had to modify the source in  
accordance with the links mentioned in the original post:
> ttp://blur.compbio.ucsf.edu/pipermail/dock-fans/2008-July/001672.html
> http://blur.compbio.ucsf.edu/pipermail/dock-fans/2008-September/001706.html

Once the headers were fixed all went swimmingly...
Specifics

in amber_types.h
add
#include <cstring>
#include <climits>

in conf_gen.h
add
#include <climits>
convert
#include <string> to #include <cstring>

in dockmol.h, sphere.h, and utils.h
convert
#include <string> to #include <cstring>

all files are found in src/dock

Hope this helps,
--Jim

On Mar 16, 2009, at 2:00 PM, dock-fans-request at docking.org wrote:

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>   1. Re: Dock-fans Digest, Vol 58, Issue 12 (William Stone)
>   2. Help: is this an error? (thirsty)
>   3. Re: Help: is this an error? (CAI Qixu)
>
> From: William Stone <drbillstone at gmail.com>
> Date: March 15, 2009 7:46:19 PM CDT
> To: dock-fans at docking.org
> Subject: Re: [Dock-fans] Dock-fans Digest, Vol 58, Issue 12
>
>
> Hi Jim:
>
> This remains a problem for me as well. Has anyone been successful at  
> installing dock6.2 on ubuntu or any specific linux distro?
>
> On Sun, Mar 15, 2009 at 3:00 PM, <dock-fans-request at docking.org>  
> wrote:
> Send Dock-fans mailing list submissions to
>        dock-fans at docking.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
>        http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> or, via email, send a message with subject or body 'help' to
>        dock-fans-request at docking.org
>
> You can reach the person managing the list at
>        dock-fans-owner at docking.org
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Dock-fans digest..."
>
>
> Today's Topics:
>
>   1. GCC 4.3 and compiling Dock 6.2 errors (Jim Parker)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 15 Mar 2009 12:46:16 -0500
> From: Jim Parker <jim.parker at prismsciences.com>
> Subject: [Dock-fans] GCC 4.3 and compiling Dock 6.2 errors
> To: dock-fans at docking.org
> Message-ID: <49BD3EE8.4070208 at prismsciences.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> For the dock maintainers,
>  This past weekend I attempted to compile Dock 6.2 on an Ubuntu system
> which among other upgrades uses gcc-4.3.2.  The problem is that gcc  
> 4.3
> has been "improved" to simplify the system header dependencies
>
> see link
> http://gcc.gnu.org/gcc-4.3/porting_to.html
>
> The result is that several #include directives have to be added to the
> .h files in order to get dock to compile -- doing some searching of  
> the
> archives this was addressed here.
>
> http://blur.compbio.ucsf.edu/pipermail/dock-fans/2008-July/001672.html
> http://blur.compbio.ucsf.edu/pipermail/dock-fans/2008-September/001706.html
>
>
> The reason for this post was just to identify the source of the errors
> (handling of header files by gcc-4.3), and find out if an updated
> version was forthcoming, or if an updated version of the source  
> would be
> desired.
>
> Cheers,
> --Jim Parker
>
>
>
> ------------------------------
>
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>
>
> End of Dock-fans Digest, Vol 58, Issue 12
> *****************************************
>
>
>
> -- 
> Bill Stone, PhD
> Office phone: 1-423-439-8762
>
>
>
> From: thirsty <thirstymail at gmail.com>
> Date: March 15, 2009 10:08:45 PM CDT
> To: dock-fans at docking.org
> Subject: [Dock-fans] Help: is this an error?
>
>
> I found this from dock 6.2 user manual:
>
>
> "gbsa_hawkins_score_cont_vdw_and_es [yes] (yes, no):
> #Flag to determine whether vdw and es values will be
> #calculated continuously or from a grid
> (if gbsa_hawkins_score_cont_vdw_and_es = yes)
>
> gbsa_hawkins_score_vdw_att_exp [6] (int):
> #VDW Lennard-Jones potential attractive exponent
> gbsa_hawkins_score_vdw_att_exp [12] (int):
> #VDW Lennard-Jones potential repulsive exponent"
> The last line, is same as the upper, why? is this an error in "ATT" ?
>
> Thank you!
>
> GuanXin
> 2009.3.16
>
>
>
>
> From: CAI Qixu <caiqixu at gmail.com>
> Date: March 16, 2009 6:31:32 AM CDT
> To: dock-fans at docking.org
> Subject: Re: [Dock-fans] Help: is this an error?
>
>
> Hi GuanXi,
> The correct one is like this:
>     gbsa_hawkins_score_vdw_att_exp [6] (int):
>     gbsa_hawkins_score_vdw_rep_exp [12] (int):
> Good luck!
>
>
> On Mon, Mar 16, 2009 at 11:08 AM, thirsty <thirstymail at gmail.com>  
> wrote:
> I found this from dock 6.2 user manual:
>
>
> "gbsa_hawkins_score_cont_vdw_and_es [yes] (yes, no):
> #Flag to determine whether vdw and es values will be
> #calculated continuously or from a grid
> (if gbsa_hawkins_score_cont_vdw_and_es = yes)
>
> gbsa_hawkins_score_vdw_att_exp [6] (int):
> #VDW Lennard-Jones potential attractive exponent
> gbsa_hawkins_score_vdw_att_exp [12] (int):
> #VDW Lennard-Jones potential repulsive exponent"
> The last line, is same as the upper, why? is this an error in "ATT" ?
>
> Thank you!
>
> GuanXin
> 2009.3.16
>
>
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>
>
>
>
> -- 
> Cai Qixu
> Email: caiqixu at gmail.com
>
>
>
> -- 
> Cai Qixu
> Email: caiqixu at gmail.com
>
>
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans

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