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.m...@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@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.war...@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.war...@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-boun...@gromacs.org [mailto: > gmx-users-boun...@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**** > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- 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 : monu46...@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 : monu46...@yahoo.com
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
