[gmx-users] mdrun: In option s, required option was not provided and the default file 'topol' does not exist or not accessible and non-integer charges

[Justin Lemkul]

On 8/1/19 7:04 PM, Mohammed I Sorour wrote:
>> Hi,
>
> that's what the ls -l prints,
>
>
>
>
>> ls -l
>> total 193120
>> drwxr-xr-x 2 tuf73544 chem     4096 Jul 26 17:20 amber99sb_dyes.ff
>> -rw-r--r-- 1 tuf73544 chem 61421681 Jul 31 19:56 em.gro
>> -rw-r--r-- 1 tuf73544 chem      191 Aug  1 15:04 equilibration_NVT_script
>> -rw-r--r-- 1 tuf73544 chem 61421681 Jul 31 19:11 full_solv_ions.gro
>> -rw-r--r-- 1 tuf73544 chem     2164 Jul  8  2016 ions.itp
>> -rw-r--r-- 1 tuf73544 chem 33866956 Jul 31 19:08 ions.tpr
>> -rw-r--r-- 1 tuf73544 chem    11962 Aug  1 14:57 mdout.mdp
>> -rw-r--r-- 1 tuf73544 chem    11962 Aug  1 14:56 #mdout.mdp.1#
>> -rw-r--r-- 1 tuf73544 chem     1875 Jul 27 08:22 nvt.mdp
>> -rw-r--r-- 1 tuf73544 chem 39455312 Aug  1 14:57 nvt.tpr
>> -rw------- 1 tuf73544 chem     1032 Aug  1 15:04 out
>> -rw------- 1 tuf73544 chem     2395 Aug  1 15:04 out.err
>> -rw-r--r-- 1 tuf73544 chem    38899 Jul 31 18:58 posre_DNA_chain_A.itp
>> -rw-r--r-- 1 tuf73544 chem    39953 Jul 31 18:58 posre_DNA_chain_B.itp
>> -rw-r--r-- 1 tuf73544 chem     3215 Aug  1 14:57 residuetypes.dat
>> -rw-r--r-- 1 tuf73544 chem     4873 Jul 18 13:03 specbond.dat
>> -rw-r--r-- 1 tuf73544 chem    69176 Jul 16 11:40 tip3p.gro
>> -rw-r--r-- 1 tuf73544 chem   588482 Jul 31 18:58 topol_DNA_chain_A.itp
>> -rw-r--r-- 1 tuf73544 chem   589283 Jul 31 18:58 topol_DNA_chain_B.itp
>> -rw------- 1 tuf73544 chem     1264 Jul 31 19:10 topol.top
>> drwxr-xr-x 3 tuf73544 chem     4096 Aug  1 14:18 trial

Are you executing mdrun interactively, or via some kind of queuing 
system with a submission script?

Also you should *not* be running dynamics on a system with such a net 
charge. Add salt and neutralize! It's not the source of your problem, 
though.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
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