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Bug #3301

pdb2gmx adding hydrogen

Added by Samuel Murail 9 months ago.

Status:
New
Priority:
Normal
Assignee:
-
Category:
preprocessing (pdb2gmx,grompp)
Target version:
-
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

After using pdb2gmx I have abberant values for hydrogen coordinates:

Input D.pdb:
```
ATOM 0 CH3 ACE P 0 0.000 0.000 0.000 0.00 0.00
ATOM 1 O ACE P 0 2.400 0.000 0.000 0.00 0.00
ATOM 2 C ACE P 0 1.359 -0.655 0.000 0.00 0.00
ATOM 3 N ASP P 1 1.431 -1.943 -0.000 0.00 0.00
ATOM 4 CA ASP P 1 2.718 -2.631 -0.000 0.00 0.00
ATOM 5 C ASP P 1 2.527 -4.139 -0.000 0.00 0.00
ATOM 6 O ASP P 1 1.410 -4.655 -0.000 0.00 0.00
ATOM 7 CB ASP P 1 3.504 -2.140 1.205 0.00 0.00
ATOM 8 CG ASP P 1 4.935 -2.691 1.357 0.00 0.00
ATOM 9 OD1 ASP P 1 5.613 -2.871 0.346 0.00 0.00
ATOM 10 OD2 ASP P 1 5.406 -2.997 2.451 0.00 0.00
TER
```

Command:

echo -e "3 \n 1\n" | gmx pdb2gmx -f D.pdb -o D_pdb2gmx.pdb -p D_pdb2gmx.top -i D_posre.itp -water tip3p -ignh -ter -vsite hydrogens -ff charmm27

I use Charmm27 ff, termini "None" for ACE and COOH for C-ter.

The output is normal except for the last hydrogen which x coor value is huge (-4092030.250 Å):

```
TITLE GROwing Monsters And Cloning Shrimps
MODEL 1
ATOM 1 1MCH ACE P 0 -0.244 -0.352 0.000 1.00 0.00 M
ATOM 2 2MCH ACE P 0 0.123 0.410 0.000 1.00 0.00 M
ATOM 3 CH3 ACE P 0 0.000 0.000 0.000 1.00 0.00 C
ATOM 4 1HH3 ACE P 0 -0.710 -0.705 0.000 1.00 0.00
ATOM 5 2HH3 ACE P 0 -0.096 0.569 0.816 1.00 0.00
ATOM 6 3HH3 ACE P 0 -0.096 0.569 -0.816 1.00 0.00
ATOM 7 C ACE P 0 1.359 -0.655 0.000 1.00 0.00 C
ATOM 8 O ACE P 0 2.400 0.000 0.000 1.00 0.00 O
ATOM 9 N ASP P 1 1.431 -1.943 -0.000 1.00 0.00 N
ATOM 10 HN ASP P 1 0.588 -2.481 0.000 1.00 0.00
ATOM 11 CA ASP P 1 2.718 -2.631 -0.000 1.00 0.00 C
ATOM 12 HA ASP P 1 3.203 -2.401 -0.844 1.00 0.00
ATOM 13 CB ASP P 1 3.504 -2.140 1.205 1.00 0.00 C
ATOM 14 HB1 ASP P 1 3.561 -1.144 1.140 1.00 0.00
ATOM 15 HB2 ASP P 1 2.986 -2.392 2.023 1.00 0.00
ATOM 16 CG ASP P 1 4.935 -2.691 1.357 1.00 0.00 C
ATOM 17 OD1 ASP P 1 5.613 -2.871 0.346 1.00 0.00 O
ATOM 18 OD2 ASP P 1 5.406 -2.997 2.451 1.00 0.00 O
ATOM 19 C ASP P 1 2.527 -4.139 -0.000 1.00 0.00 C
ATOM 20 OT1 ASP P 1 1.410 -4.655 -0.000 1.00 0.00 O
ATOM 21 OT2 ASP P 1 3.652 -4.904 0.000 1.00 0.00
ATOM 22 HT2 ASP P 1 -4092030.250 -0.943 0.000 1.00 0.00
TER
ENDMDL
```

cheers

Also available in: Atom PDF