[gmx-users] Test-set

[Justin A. Lemkul]

Any clues from any of the other *.out files?

-Justin

Zhanglin Ni wrote:
> 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" <jalemkul at 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 at gromacs.org>
>> Message-ID: <4A02BF09.4050502 at 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
>>
>> ========================================
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before 
>> posting!
>>
>> End of gmx-users Digest, Vol 61, Issue 21
>> *****************************************
>>
> 
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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

========================================