Alan wrote:
Hi Justin,
Please, confirm this, you mean that this pdb worked for you with '-ignh'?
Gosh...
Correct.
So I may not loosing my mind when I said that it was working before.
So, I am running:
- Mac Osx 10.5.7 intel.
- Gromacs 4.0.5 (from Fink) with ffamber;
- Compilers from Fink.
Identical to my system, except I compiled from source. Perhaps the fink package
is broken?
-Justin
I ran test suite and although I got some fails for complex and
kernel, nothing for simple or pdb2gmx.? Anyway, I doubt tested suite
would fail because oplsaa is working fine here if I do 'pdb2gmx -f
GGG.pdb -ff oplsaa -ignh'
In any case, many thanks for your attention Justin,
Alan
On Mon, Jun 15, 2009 at 20:01, <[email protected]> wrote:
Alan wrote:
Thank you Justin,
You noticed well that. But this example was built to work without
-ignh and to exemplify my problem, because in real case I have this
protein and either I can use 'sed' to fix it (mainly H names) I found
it annoying sometimes, so why not -ignh?
No idea. I can successfully process your .pdb file with and without -ignh, and
I get the same result (a correct topology) each time. Have you run the test
suite to validate your installation? Maybe if you post the details of your
hardware, compilers, OS, etc. someone can spot something that might be
problematic (i.e., a bug).
-Justin
Cheers,
Alan
On Mon, Jun 15, 2009 at 15:51, <[email protected]> wrote:
Alan wrote:
Hi there,
I am trying to understand why when doing:
pdb2gmx -f GGG.pdb -ff amber99sb -ignh
I am getting:
WARNING: atom H is missing in residue GLY 2 in the pdb file
You might need to add atom H to the hydrogen database of residue GLY
in the file ff???.hdb (see the manual)
I don't know why this is failing, but from the looks of your .pdb file, you have
all the atoms you need, properly named and everything. Why do you need -ignh?
-Justin
-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.5
Source code file: pdb2top.c, line: 704
Fatal error:
There were 1 missing atoms in molecule Protein_G, if you want to use
this incomplete topology anyhow, use the option -missing
-------------------------------------------------------
in /sw/share/gromacs/top/ffamber99sb.hdb I have:
GLY 2
1 1 H N -C CA
2 6 HA CA N C
And I see nothing wrong with that.
in /sw/share/gromacs/top/ffamber99sb.rtp:
[ GLY ]
[ atoms ]
N amber99_34 -0.41570 1
H amber99_17 0.27190 2
CA amber99_11 -0.02520 3
HA1 amber99_19 0.06980 4
HA2 amber99_19 0.06980 5
C amber99_2 0.59730 6
O amber99_41 -0.56790 7
Which is pretty OK too.
Besides, I don't get any error for NGLY or CGLY. Only "atom H is
missing in residue GLY 2". If I mess with ffamber99sb.hdb for GLY I
got others messages stating the other missing atoms.
OPLS, which is very similar, works fine.
The pdb is as simple as this:
ATOM 1 N NGLYG 1 59.012 0.129 -0.254 1.00 0.00
ATOM 2 H1 NGLYG 1 58.484 0.488 0.618 1.00 0.00
ATOM 3 H2 NGLYG 1 58.683 0.775 -1.007 1.00 0.00
ATOM 4 H3 NGLYG 1 58.789 -0.895 -0.326 1.00 0.00
ATOM 5 CA NGLYG 1 60.467 0.239 -0.366 1.00 0.00
ATOM 6 HA1 NGLYG 1 60.728 1.248 -0.251 1.00 0.00
ATOM 7 HA2 NGLYG 1 60.773 -0.150 -1.355 1.00 0.00
ATOM 8 C NGLYG 1 61.175 -0.584 0.690 1.00 0.00
ATOM 9 O NGLYG 1 60.636 -0.753 1.809 1.00 0.00
ATOM 10 N GLY G 2 62.471 -1.163 0.322 1.00 0.00
ATOM 11 H GLY G 2 62.882 -1.173 -0.678 1.00 0.00
ATOM 12 CA GLY G 2 63.150 -1.717 1.498 1.00 0.00
ATOM 13 HA1 GLY G 2 62.745 -2.672 1.656 1.00 0.00
ATOM 14 HA2 GLY G 2 63.047 -1.068 2.389 1.00 0.00
ATOM 15 C GLY G 2 64.648 -1.799 1.285 1.00 0.00
ATOM 16 O GLY G 2 65.151 -2.016 0.165 1.00 0.00
ATOM 17 N CGLYG 3 65.503 -1.595 2.460 1.00 0.00
ATOM 18 H CGLYG 3 65.152 -1.325 3.447 1.00 0.00
ATOM 19 CA CGLYG 3 66.902 -1.817 2.091 1.00 0.00
ATOM 20 HA1 CGLYG 3 67.178 -1.043 1.438 1.00 0.00
ATOM 21 HA2 CGLYG 3 67.022 -2.819 1.632 1.00 0.00
ATOM 22 C CGLYG 3 67.808 -1.809 3.299 1.00 0.00
ATOM 23 OC1 CGLYG 3 67.222 -1.605 4.509 1.00 0.00
ATOM 24 OC2 CGLYG 3 69.135 -2.006 3.077 1.00 0.00
My memory may fail, but I can swear it was working before...
Many thanks in advance,
Alan
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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