[gmx-users] Re: Problem in atom name correspondence between protein topology and coordinates after mutation grompp

[David van der Spoel]

himanshu khandelia wrote:
> 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
pdb2gmx reorders atoms according to the order in the rtp file. You 
should not ignore those warnings, because you ill have a twisted sidechain.

> ######################
> 
> On Nov 30, 2007 3:30 PM, himanshu khandelia <hkhandelia at gmail.com> 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
>>
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se