tnx for your help Justin! but shouldn't the topology of S atom be described for gromacs? unless gromacs may know P atom with the same topology as S. although they may not be the same!? regards sajad
________________________________ From: Justin A. Lemkul <jalem...@vt.edu> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Sat, April 23, 2011 5:54:58 AM Subject: Re: [gmx-users] dealing with ATP Sajad Ahrari wrote: > Dear users > i am working with a protein witch holds a hetero-atom in it's pdb structure. >the hetero-atom is named "d" and stands for "ADP+SO4" (in fact the third >phosphate of ATP is being substituted with SO4). i wanted to know if gromacs >holds a feature to change "d" into ATP? and if so do > No, but you can use a text editor to replace the S atom with P. > i need to introduce ATP for Gromacs or it is known for the program? Some force fields support ATP, some do not. Check the .rtp files and see what you find. -Justin > i do appreciate your help! > sajad > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
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