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

[Qing Lv]

My protein contains 2 chains, and ILE294 is the C-terminus of chain 1. When I used pdb2gmx to process the GRO file, it can recognize N-terminus of chain 1 and C-terminus of chain 2, but cannot recognize C-terminus of chain 1. Since there is no chain separators in GRO files (like "TER" in PDB), pdb2gmx might regard all aminoacids as one single chain.
Sorry for not having explained clearly in previous emails. Any suggestions?


Many thanks,
Qing


At 2017-06-23 16:24:13, "Qing Lv" <lvqingjiejie at 163.com> wrote:
>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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