[gmx-users] Error in pdb2gmx

[Justin Lemkul]

On 4/30/13 6:10 AM, Nikunj Maheshwari wrote:
> Thanks Justin. I know that using -ignh will solve the problem. But I was
> just curious because I got the same error message ("Fatal error: Atom HD1
> in residue HIS 65 was not found in rtp entry HISE with 17 atoms while
> sorting atoms. ") when I used OPLS, this time it was His 65.
>
> So I used -his option in pdb2gmx and got the following options to choose
>
> Which HISTIDINE type do you want for residue 65
> 0. H on ND1 only (HISD)           #Works. total charge= -17.000
> 1. H on NE2 only (HISE)           # Error
> 2. H on ND1 and NE2 (HISH)    #Works. total charge= -16.000
> 3. Coupled to Heme (HIS1)       #Works. total charge= -17.000
>
> So shall I go ahead with any of the option except 1, or use -ignh?
>

In this case, pdb2gmx is detecting that you should have epsilon-protonated 
histidine at His65, but the proton is at the delta position, so there is a 
conflict.  HISD and HISH work because they both should have a proton on ND1.

-Justin

> On Tue, Apr 30, 2013 at 3:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 4/30/13 2:59 AM, Nikunj Maheshwari wrote:
>>
>>> Dear all,
>>>
>>> I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o
>>> output.gro)
>>>
>>> I used 13. GROMOS 53a6 force field
>>>
>>> "Fatal error:
>>> Atom HA in residue GLU 1 was not found in rtp entry GLU with 12 atoms
>>> while
>>> sorting atoms.
>>>
>>> For a hydrogen, this can be a different protonation state, or it
>>> might have had a different number in the PDB file and was rebuilt
>>> (it might for instance have been H3, and we only expected H1 & H2).
>>> Note that hydrogens might have been added to the entry for the N-terminus.
>>> Remove this hydrogen or choose a different protonation state to solve it.
>>> Option -ignh will ignore all hydrogens in the input."
>>>
>>> So I used -glu option in pdb2gmx (pdb2gmx -f 123.pdb -o output.gro -glu)
>>>
>>> I get the following options.
>>>
>>> Which GLUTAMIC ACID type do you want for residue 1
>>> 0. Not protonated (charge -1) (GLU)
>>> 1. Protonated (charge 0) (GLUH)
>>>
>>> Both options give the same error as before.
>>>
>>> The same error occurs for HB1 as well.
>>>
>>> Will I have to edit the pdb or rtp file? Or any other suggestions?
>>>
>>>
>> Read the error message again; it tells you what to do.
>>
>> Consider what you're doing - you're supplying a united-atom force field
>> with an all-atom structure.  The chosen parameter set doesn't have explicit
>> hydrogens on nonpolar groups.  Hence pdb2gmx complains that you're giving
>> it atoms it doesn't understand.  Use of -ignh solves this issue, which is
>> precisely what the error message is telling you.
>>
>> -Justin
>>
>> --
>> ==============================**==========
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
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-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================