[gmx-users] Error in pdb2gmx

Nikunj Maheshwari nixcrazyforher at gmail.com
Tue Apr 30 12:10:28 CEST 2013

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?

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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