Thanks for your reply.
I checked the checkpot.out file.
It didnot show the any energy values but
"
comparing energy file reference_s.edr and ener.edr
There are 30 terms in the energy files
There are 3 terms to compare in the energy files
Files read succesfully
"
what the problem could be. Thanks.
Johnny
Zhanglin Ni wrote:
Dear all,
I installed gromacs-4.0.4, I followed the installation instruction. the
installation seemed no problem at all. afterwards, I run test-set
gmxtest-4.0.4 immediately.
The results are
All 16 simple tests PASSED
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in tip4pflex
FAILED. Check files in water
4 out of 14 complex tests FAILED
So check the output of these tests; small rounding errors are
insignificant and
can cause the test to fail (as described on the wiki).
The kernel failures you cite below have been reported before:
http://bugzilla.gromacs.org/show_bug.cgi?id=313
-Justin
FAILED. Check files in kernel020
FAILED. Check files in kernel120
FAILED. Check files in kernel121
FAILED. Check files in kernel122
FAILED. Check files in kernel123
FAILED. Check files in kernel124
FAILED. Check files in kernel220
FAILED. Check files in kernel221
FAILED. Check files in kernel222
FAILED. Check files in kernel223
FAILED. Check files in kernel224
FAILED. Check files in kernel320
FAILED. Check files in kernel321
FAILED. Check files in kernel322
FAILED. Check files in kernel323
FAILED. Check files in kernel324
16 out of 63 kernel tests FAILED
pdb2gmx tests PASSED
How I can do to solve the problem since it was just installed. Thanks
Johnny
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--
========================================
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
========================================
------------------------------
Message: 6
Date: Thu, 07 May 2009 06:59:21 -0400
From: "Justin A. Lemkul" <jalem...@vt.edu>
Subject: Re: [gmx-users] atom name O3PB not found in residue ATP 340
while generating exclusions when running pdb2gmx
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4a02bf09.4050...@vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Una Bjarnadottir wrote:
Dear all,
I'm running a simulation of a structure which has part of ATP bound to
it so I'm using the -missing command when running pdb2gmx
pdb2gmx runs and lists the missing atoms and than it gives a fatal error
about missing atom name!
WARNING: atom O3PB is missing in residue ATP 340 in the pdb file
WARNING: atom APG is missing in residue ATP 340 in the pdb file
WARNING: atom O1PG is missing in residue ATP 340 in the pdb file
WARNING: atom O2PG is missing in residue ATP 340 in the pdb file
WARNING: atom O3PG is missing in residue ATP 340 in the pdb file
WARNING: atom H3PG is missing in residue ATP 340 in the pdb file
You might need to add atom H3PG to the hydrogen database of
residue ATP
in the file ff???.hdb (see the manual)
There were 17 missing atoms in molecule Protein_A
Number of bonds was 3730, now 3725
Generating angles, dihedrals and pairs...
Fatal error: atom name O3PB not found in residue ATP 340 while
generating exclusions
The [ exclusions ] are pre-defined in the force field .rtp file. The
easiest
way I can see to get around this is to make a local copy of the .rtp file,
make
a new entry for your molecule based on the ATP entry (deleting out
whatever
atoms are not present) and trying again, using a new name for this partial
ATP,
in both the .rtp and .pdb files.
The -missing option, as described by pdb2gmx is "dangerous" for this
reason.
-Justin
How can I resolve this first not done by -missing command?
Cheers, Una
--
========================================
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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End of gmx-users Digest, Vol 61, Issue 21
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