[gmx-users] Re:problem adding H atoms
Justin A. Lemkul
jalemkul at vt.edu
Fri Sep 17 16:40:54 CEST 2010
Stacey Meadley wrote:
> Hi Justin,
> the gromacs version is 4.0.4.
> command line: pdb2gmx -f 1B9Eostate.pdb -o 1B9Eostate.gro -p
> 1B9Eostate.top -ff amber03
> message: WARNING: atom H is missing in residue ILE 2 in the pdb file
> You might need to add atom H to the hydrogen database of
> residue ILE
> in the file ff???.hdb (see the manual)
> beginning of pdb file:
> ATOM 1 N NGLYA 1 -5.201 9.673 -2.852 1.00 21.99
> N
> ATOM 2 CA NGLYA 1 -3.724 9.368 -2.711 1.00 21.30
> C
> ATOM 3 C NGLYA 1 -3.320 8.030 -3.324 1.00 18.48
> C
> ATOM 4 O NGLYA 1 -4.164 7.323 -3.878 1.00 24.81
> O
> ATOM 5 N ILE A 2 -2.065 7.644 -3.159 1.00 13.65
> N
> ATOM 6 CA ILE A 2 -1.579 6.399 -3.716 1.00 12.18
> C
> ATOM 7 C ILE A 2 -2.254 5.174 -3.077 1.00 15.61
> C
> ATOM 8 O ILE A 2 -2.629 4.249 -3.786 1.00 13.09
> O
> ATOM 9 CB ILE A 2 -0.037 6.325 -3.601 1.00 12.48
> C
> ATOM 10 CG1 ILE A 2 0.494 5.122 -4.357 1.00 14.27
> C
> ATOM 11 CG2 ILE A 2 0.397 6.250 -2.171 1.00 7.71
> C
> ATOM 12 CD ILE A 2 1.946 5.193 -4.618 1.00 11.64
> C
> ATOM 13 N VAL A 3 -2.487 5.202 -1.759 1.00 19.67
> N
> ATOM 14 CA VAL A 3 -3.123 4.072 -1.065 1.00 21.16
> C
> ATOM 15 C VAL A 3 -4.531 3.814 -1.605 1.00 21.76
> C
> ATOM 16 O VAL A 3 -4.954 2.670 -1.806 1.00 20.69
> O
> ATOM 17 CB VAL A 3 -3.225 4.312 0.465 1.00 21.43
> C
> ATOM 18 CG1 VAL A 3 -3.687 3.033 1.165 1.00 21.34
> C
> ATOM 19 CG2 VAL A 3 -1.885 4.782 1.039 1.00 19.65
> C
>
I can't reproduce this problem. I made a slight modification to the coordinates
you posted to build CVAL so I could process the structure. It worked fine with
version 4.0.7 (I don't have 4.0.4 installed any more).
I would recommend that you upgrade to the latest version (4.5.1) instead of one
that is over a year and a half old. The biggest benefit (aside from bug fixes)
is that the Amber force fields are now natively supported, no more manual
editing of residue names, termini, etc.
If the problem persists (which it shouldn't, as I have also processed the file
with version 4.5.1), then post again with the results.
-Justin
P.S. If you want to test what I did, here's the .pdb file I used. I opened
yours in xLeap to build the termini.
TITLE Giving Russians Opium May Alter Current Situation
MODEL 1
ATOM 1 N NGLYA 1 -5.201 9.673 -2.852 1.00 0.00 N
ATOM 2 CA NGLYA 1 -3.724 9.368 -2.711 1.00 0.00 C
ATOM 3 C NGLYA 1 -3.320 8.030 -3.324 1.00 0.00 C
ATOM 4 O NGLYA 1 -4.164 7.323 -3.878 1.00 0.00 O
ATOM 5 N ILE A 2 -2.065 7.644 -3.159 1.00 0.00 N
ATOM 6 CA ILE A 2 -1.579 6.399 -3.716 1.00 0.00 C
ATOM 7 CB ILE A 2 -0.037 6.325 -3.601 1.00 0.00 C
ATOM 8 CG2 ILE A 2 0.397 6.250 -2.171 1.00 0.00 C
ATOM 9 CG1 ILE A 2 0.494 5.122 -4.357 1.00 0.00 C
ATOM 10 CD1 ILE A 2 2.013 5.071 -4.229 1.00 0.00 C
ATOM 13 CD ILE A 2 1.946 5.193 -4.618 1.00 0.00 C
ATOM 11 C ILE A 2 -2.254 5.174 -3.077 1.00 0.00 C
ATOM 12 O ILE A 2 -2.629 4.249 -3.786 1.00 0.00 O
ATOM 14 N CVALA 3 -2.487 5.202 -1.759 1.00 0.00 N
ATOM 15 CA CVALA 3 -3.123 4.072 -1.065 1.00 0.00 C
ATOM 16 CB CVALA 3 -3.225 4.312 0.465 1.00 0.00 C
ATOM 17 CG1 CVALA 3 -3.687 3.033 1.165 1.00 0.00 C
ATOM 18 CG2 CVALA 3 -1.885 4.782 1.039 1.00 0.00 C
ATOM 19 C CVALA 3 -4.531 3.814 -1.605 1.00 0.00 C
ATOM 20 OC1 CVALA 3 -4.954 2.670 -1.806 1.00 0.00 O
ATOM 21 OC2 CVALA 3 -5.294 4.751 -1.829 1.00 0.00 O
TER
ENDMDL
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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