[gmx-users] overriding -ignh flag

[Justin Lemkul]

On 2/5/20 1:46 PM, Yogesh Sharma wrote:
> hi everyone,
> I want to override  -ignh tag as this tag is stripping hydrogens off amino
> acid side chains, which might incorporate artifacts. my N and C terminals
> are NH3+ and coo-
>
> gmx pdb2gmx -f y.pdb  -o y_pro.gro  -water spc -his -ter
> i am getting Fatal error:
> Atom HA in residue MET 1 was not found in rtp entry MET with 11 atoms while
> sorting atoms.
>
> ATOM      1  N   MET X   1      36.214  42.372  20.531  0.00  0.00
>
> ATOM      2  HT1 MET X   1      35.813  41.445  20.781  0.00  0.00
>
> ATOM      3  HT2 MET X   1      35.746  42.657  19.648  0.00  0.00
>
> ATOM      4  HT3 MET X   1      35.967  43.009  21.315  0.00  0.00
>
> ATOM      5  CA  MET X   1      37.678  42.198  20.410  0.00  0.00
>
> ATOM      6  HA  MET X   1      38.179  43.150  20.502  0.00  0.00
>
> ATOM      7  CB  MET X   1      38.105  41.245  21.499  0.00  0.00
>
> ATOM      8  HB1 MET X   1      38.862  40.523  21.124  0.00  0.00
>
> ATOM      9  HB2 MET X   1      37.271  40.587  21.823  0.00  0.00
>
> ATOM     10  CG  MET X   1      38.740  41.847  22.761  0.00  0.00
>
> ATOM     11  HG1 MET X   1      39.031  40.967  23.374  0.00  0.00
>
> ATOM     12  HG2 MET X   1      38.131  42.586  23.324  0.00  0.00
>
> ATOM     13  SD  MET X   1      40.389  42.642  22.497  0.00  0.00
>
> ATOM     14  CE  MET X   1      40.740  42.470  24.299  0.00  0.00
>
> ATOM     15  HE1 MET X   1      40.704  41.389  24.553  0.00  0.00
>
> ATOM     16  HE2 MET X   1      40.132  43.023  25.047  0.00  0.00
>
> ATOM     17  HE3 MET X   1      41.809  42.739  24.433  0.00  0.00
>
> ATOM     18  C   MET X   1      38.114  41.717  19.047  0.00  0.00
>
> ATOM     19  O   MET X   1      37.405  40.927  18.465  0.00  0.00
> HA is not even NH3+ hydrogen. what should be the appropriate  nomenclature
> here? Many of hydrogen atoms are not listed in .rtp files. how should i
> refine my pdb without compromising with hydrogens?

You don't say which force field you're using but if the H atoms aren't 
in the .rtp file that means you're using a united-atom force field (e.g. 
GROMOS) and that is precisely what the force field requires. UA force 
fields do not have aliphatic H atoms, including HA.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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