[gmx-users] Test-set

Zhanglin Ni zlni at u.washington.edu
Thu May 7 17:41:37 CEST 2009


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
>
> ========================================
>
>
> ------------------------------
>
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>
> End of gmx-users Digest, Vol 61, Issue 21
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