Hi,
Ok, but why I am not able to continue my MD using this rst file?
/Urszula Uciechowska
> Hi
>
> I guess you need to re-imaging back the primary box.
> This is well explained in Tutorial B1 Section 5, at the end when they
> explain how to visualize a trajectory.
> (You need to write a simple script and run it in cpptraj).
>
> In addition, which option do you use in vmd when you load the mdcrd file?
> You have to option and I think you shoul use as format " Amber coordinates
> with Periodic Box". Did you already use this format?
>
> Hope this help.
>
> Valentina
> _______________________________
> Valentina Romano | PhD Student |
> Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics |
> Klingelbergstrasse 61 | CH-4056 Basel |
>
> Phone: +41 61 267 15 80
>
>
> ________________________________________
> From: Urszula Uciechowska [urszula.uciechowska.biotech.ug.edu.pl]
> Sent: Wednesday, August 20, 2014 12:55 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] error ambpdb - Old style inpcrd file read
>
> To my previous question: I attached a picture from vmd where I simply
> loaded the prmtop and mdcrd file and this is what I got... the water is
> very strange. What could be the problem?
>
> Thank you in advance for your help.
>
> /Urszula Uciechowska
>
>> Dear AMBEr users,
>>
>> I am not able to convert my *.rst file into the *pdb - the command I
>> used
>> is ambpdb -p prmtop <*rst> *.pdb. It is very strange as the simulations
>> are run for 30ns.
>> after running ambpdb -I have
>>
>> | New format PARM file being parsed.
>> | Version = 1.000 Date = 04/09/14 Time = 15:01:14
>> forrtl: severe (64): input conversion error, unit 5, file stdin
>> Image PC Routine Line
>> Source
>> libintlc.so.5 00007FF4C016B9AA Unknown Unknown
>> Unknown
>> libintlc.so.5 00007FF4C016A4A6 Unknown Unknown
>> Unknown
>> libifcore.so.5 00007FF4C11297AC Unknown Unknown
>> Unknown
>> libifcore.so.5 00007FF4C109CE42 Unknown Unknown
>> Unknown
>> libifcore.so.5 00007FF4C109C2E6 Unknown Unknown
>> Unknown
>> libifcore.so.5 00007FF4C10D7C34 Unknown Unknown
>> Unknown
>> ambpdb 0000000000410E0D Unknown Unknown
>> Unknown
>> ambpdb 0000000000404325 Unknown Unknown
>> Unknown
>> ambpdb 000000000040120C Unknown Unknown
>> Unknown
>> libc.so.6 00007FF4BFC0F1A6 Unknown Unknown
>> Unknown
>> ambpdb 0000000000401109 Unknown Unknown
>> Unknown
>>
>> I have chcecked the *rst file and seems to be ok and the simulations
>> finished correctly. However when I try to use this *rst file for the
>> next
>> production run I got an error in *out file:
>>
>> | Flags: MPI
>> getting new box info from bottom of inpcrd
>> | INFO: Old style inpcrd file read
>>
>> and simulations stoped.
>>
>> the input file:
>> production
>> production
>> &cntrl
>> imin = 0, irest = 1, ntx = 7,
>> ntb = 2, pres0 = 1.0, ntp = 1,
>> taup = 2.0,
>> cut = 10, ntr = 0,
>> ntc = 2, ntf = 2,
>> tempi = 298.15, temp0 = 298.15,
>> ntt = 3, gamma_ln = 1.0,
>> nstlim = 250000, dt = 0.002,
>> ntpr = 200, ntwx = 200, ntwr = 200
>> /
>>
>> Any ideas why this error comes up?
>>
>>
>> Best regards
>> Urszula Uciechowska
>>
>>
>>
>>
>>
>> -----------------------------------------
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>> http://www.ug.edu.pl/
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> -----------------------------------------
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> http://www.ug.edu.pl/
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Received on Wed Aug 20 2014 - 04:30:02 PDT
