How many atoms in your system? Note the I5 format on the 2nd line of
coordinate/restart:
http://ambermd.org/formats.html#restart
FORMAT(I5,5E15.7) NATOM,TIME
If you have > 99999 atoms (5x'9'), netcdf format is your only hope.
Bill
On 2/20/17 10:19 PM, Bill Ross wrote:
> How many fields have ****? If it's only on the 2nd line, it can probably
> be fixed manually.
>
> Also you could try writing a netcdf rst.
>
> Bill
>
>
> On 2/20/17 9:55 PM, Chinh Su Tran To wrote:
>> Dear Bill,
>>
>> Thanks. Yes, it indeed is.
>> I looked at the min1.rst in text editor, the 2nd line of the resulting
>> min1.rst output contains ****, the rest looks normal. I couldn't view the
>> structure as it couldn't be converted because some format errors occurred.
>>
>> I was searching for the cause behind since it is confusing to me that the
>> bash script used for this run was applied previously and it worked.
>>
>> One note aside, in the beginning of the min1.out, there are some numerical
>> errors (represented by **** in VDWAALS results, I guess that was caused by
>> unreasonable distances in the initial structure, but it is resolved in the
>> end of the first minimization min1). Hence, I think this is not the cause.
>>
>> Please help. Thanks.
>>
>> CS
>>
>>
>>
>> On Tue, Feb 21, 2017 at 11:50 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>
>>> It's the output of the run that created the .rst that needs looking at.
>>>
>>> Bill
>>>
>>>
>>> On 2/20/17 7:33 PM, Hai Nguyen wrote:
>>>> I didn't see any wrong in my input files.
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 20 2017 - 22:30:03 PST
