Well, if you are using
>> irest=0
I find it somewhat strange that you would be using a “md.rst” file. Unless this is instead you coordinate file from leap? It also would seem that the error message explains part of the problem, there is a missmatch between the content of the md.rst file and the topology file.
What files do you have, what command are you running when you encounter the error and have you initiated with an energy minimisation run and equilibrated the temperature and pressure of the system before trying to run the input below?
Best regards
// Gustaf
> On 1 Sep 2020, at 15:12, Kehinde Idowu <kidowu93.yahoo.com> wrote:
>
> Thanks for your response. My md.out file say "ERROR: I could not find enough coordinates in md.rst". I have repeated the md simulation over and over, I keep get the same message.
> On Tuesday, September 1, 2020, 11:40:42 AM GMT+2, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> Have you looked at your mdout file?
>
> Does it run longer if you set tempi and temp0 to 100?
>
> Bill
>
> On 9/1/20 2:12 AM, Kehinde Idowu wrote:
>>> Good day all
>>> Please, I am running a protein-protein md simulation onAmber 18
>>> my md is being terminated, here is this error message Igot from my md_error file “TOP PMEMD Terminated Abnormally!”
>>> My md.in looks as follow;
>>
>>
>>> Equilibration Step of MMP3 (MMMM): stage-1
>> &cntrl
>>
>>> imin= 0,
>> iwrap=1,
>>
>> irest=0,
>>
>> NTX=1,
>>
>> ntb=2,
>>
>> ntp=1,
>>
>> PRES0=1.0,
>>
>> TAUP=2.0,
>>
>> NTPR=500,
>>
>> NTWX=500,
>>
>> NTWR=500,
>>
>> ntr=0,
>>
>> Tempi=300.0,
>>
>> Temp0=300.0,
>>
>> NTT=3,
>>
>> gamma_ln=1.0,
>>
>> NTC=2,
>>
>> NTF=2,
>>
>> cut=12.0,
>>
>> nstlim=10000000,
>>
>> dt=0.002,
>>
>> ntxo=1,
>>
>> ioutfm=0,
>>
>> /
>>
>>
>>
>> Kindly advice on how to solve this problem.
>>
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>>
> --
> Phobrain.com
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Received on Wed Sep 02 2020 - 00:00:02 PDT
