Your procedure sounds like it could induce an error in a number of steps. Have you considered simply submitting your initial .pdb file to a program like Sybyl or DeepView and allowing it to make the mutation for you?
-Justin Quoting himanshu khandelia <[EMAIL PROTECTED]>: > Sorry, there was a little mistake in the reported output of grompp in > my previous email. It should be as follows: > > ###################### > Warning: atom names in protein.top and final.gro don't match (CD2 - HD1) > Warning: atom names in protein.top and final.gro don't match (CE1 - CD2) > Warning: atom names in protein.top and final.gro don't match (NE2 - CE1) > Warning: atom names in protein.top and final.gro don't match (HE2 - NE2) > WARNING 2 [file "protein.top", line 35]: > 4 non-matching atom names > atom names from protein.top will be used > atom names from final.gro will be ignored > ###################### > > On Nov 30, 2007 3:30 PM, himanshu khandelia <[EMAIL PROTECTED]> wrote: > > Hi Folks, > > > > I am not being able to debug a little problem. I hope someone will be > > able to point out the mistake. Here is what I am trying to do: > > > > I need to mutate a SER to a GLU residue in a protein. However, after > > mutation (and making a new topology), when I run grompp, I get the > > following error: > > > > ###################### > > processing coordinates... > > Warning: atom names in protein.top and p.gro don't match (CD2 - HD1) > > Warning: atom names in protein.top and p.gro don't match (CE1 - CD2) > > Warning: atom names in protein.top and p.gro don't match (NE2 - CE1) > > Warning: atom names in protein.top and p.gro don't match (HE2 - NE2) > > WARNING 2 [file "protein.top", line 35]: > > 4 non-matching atom names > > atom names from protein.top will be used > > atom names from final.gro will be ignored > > ###################### > > > > So, the order or names of atoms do not correspond correctly any more. > > I cannot find out why this is the case. Here are the steps that I used > > to make the mutation: > > > > ###################### > > 1. Convert the initial structure (init.gro) to a pdb (init.pdb) using > editconf > > 2. Pull out coordinates of the SER from init.pdb and change residue > > name from SER to GLU. Lets call this file residue-to-be-mutated.pdb > > 3. Rename the following atoms: (a) OG to CG (b) HG to CD in > > residue-to-be-mutated.pdb > > 4. Guess remaining coordinates (for the 2 oxygen atoms on the carboxyl > > group) in some external software > > 5. plug in the guessed coordinates into residue-to-be-mutated.pdb > > 6. Removed the coordinates of SER from init.pdb, and replaced them by > > coordinates in residue-to-be-mutated.pdb. Note that because of the > > insertion of two extra atoms, the numbering of atoms in the pdb file > > is not continuous any more. > > 7. Convert the resulting pdb file into .gro format using editconf. > > Final output is final.gro, which should have continuous numbering of > > atom numbers. > > > > 8. Then I also make a new protein topology using pdb2gmx. > > ###################### > > > > Any suggestions, anyone ? > > > > - The number of atoms in the initial and final .gro files differ by > > two, which is the same as the difference in the number of atoms > > between a SER and a GLU amino acid > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
