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
