Fwd: [gmx-users] Re: Gromacs error

[bharat gupta]

 I have another issue .. I am am preparing the structure for simulation
which is a docked complex containing Phospharylated tyrosine. I am using
Amber 99 force field and update the residuetypes.dat, aminoacid.rtp,
ffbonded.itp files for pTYR but still the error that "Residue 'PTYR' not
found in residue topology database" ... but all the changes I have made then
where else could the problem be ??

---------- Forwarded message ----------
From: bharat gupta <bharat.85.monu at gmail.com>
Date: Fri, Jun 17, 2011 at 11:18 AM
Subject: Re: [gmx-users] Re: Gromacs error
To: Discussion list for GROMACS users <gmx-users at gromacs.org>


thanks..  I fixed the problem by using the command execstack -c filename


but I have another issue .. I am am preparing the structure for simulation
which is a docked complex containing Phospharylated tyrosine. I am using
Amber 99 force field and update the residuetypes.dat, aminoacid.rtp,
ffbonded.itp files for pTYR but still the error that "Residue 'PTYR' not
found in residue topology database" ... but all the changes I have made then
where else could the problem be ??


On Fri, Jun 17, 2011 at 10:04 AM, Dallas Warren <Dallas.Warren at monash.edu>wrote:

>  Someone with some more in depth knowledge will hopefully pipe up, but
> until then there are some things you can read up on and see if it will solve
> your issue.****
>
> ** **
>
> Google is your friend.****
>
> ** **
>
> Put “error while loading shared libraries: libgmx.so.6: Permission denied”
> into it, and  you get a number of topics on forums discussing the issue you
> have had.  Not directly with libgmx.so.6 but that issue appears to be the
> same.  And they all relate to Fedora from what I can see.****
>
> ** **
>
> This one appears to solve the issue -
> http://forums.fedoraforum.org/showthread.php?t=253870****
>
> ** **
>
> With some more reading you should be able to sort out what the issue
> actually is, seems to be something to do with how files are handled with
> Fedora, and then the correct course of action.****
>
> ** **
>
> Catch ya,
>
> Dr. Dallas Warren****
>
> Medicinal Chemistry and Drug Action****
>
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at monash.edu****
>
> +61 3 9903 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to resemble a
> nail. ****
>
> ** **
>
> *From:* gmx-users-bounces at gromacs.org [mailto:
> gmx-users-bounces at gromacs.org] *On Behalf Of *bharat gupta
> *Sent:* Friday, 17 June 2011 10:40 AM
> *To:* Discussion list for GROMACS users
> *Subject:* [gmx-users] Re: Gromacs error****
>
> ** **
>
> Hi,
>
> I have installed gromacs 4.5 on fedora core 15 and whenever I try to run
> any command like pdb2gmx ...  I am getting the following error :
>
> error while loading shared libraries: libgmx.so.6: cannot enable executable
> stack as shared object requires: Permission denied
>
> Pls help??
>
>
> --
> Bharat****
>
> --
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-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com




-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
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