[gmx-users] 5-letter atom names in topology files

[Qing Lv]

Dear Mark,


Actually I had tried the method you suggested, but got such errors (pdb2gmx):
Fatal error:
Atom O1 in residue ILE 294 was not found in rtp entry ILE with 9 atoms while sorting atoms.
ILE294 is C-terminus of my protein. I looked up in aminoacids.rtp and there are no atom "O1" or "O2" in ILE entry; however, I never got such errors when using pdb2gmx to process PDB files. Maybe, pdb2gmx can only process terminal residues for PDB files?


Also, I have tried to process protein and ATP separately with pdb2gmx and then combined them together, but met problems. That's why I sent another 2 emails...


Qing


At 2017-06-23 15:33:17, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
>Hi,
>
>I suggest you produce your initial conformation in .gro format, which
>permits five-character atom names. That might mean using editconf on your
>.pdb file, and then manually renaming atoms.
>
>Mark
>
>On Fri, Jun 23, 2017 at 3:55 AM Qing Lv <lvqingjiejie at 163.com> wrote:
>
>> Hi,
>>
>>
>> Gromos 54a7 force field has built-in topologies for some small molecules,
>> like ATP. In these topologies, many atoms have names of up to 5 letters,
>> such as AO1PA and AO2PB. However, PDB files seem do not support 5-letter
>> atom names. So, if I name an atom "AO2PB" in PDB, it will be truncated to
>> "AO2P" or "O2PB" when executing pdb2gmx, and these atoms cannot be
>> recognized then.
>> Anyone know how to solvate this problem? Many thanks ^_^
>>
>>
>> Qing
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