I knew it! I should be solving crimes instead of playing with molecular dynamics simulations...
----- Mensaje original -----
De: "Ayesha Fatima" <ayeshafatima.69.gmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Viernes, 7 de Agosto 2020 10:14:08
Asunto: Re: [AMBER] tleap.in error
Dear Matias and Dr. Case
Thank you both for the emails.
I did use notepad on Windows 10. And now that you mention it, i think that
maybe the issue.
When i use the individual commands, they run fine.
Thank you for pointing that out.
I will check it out.
Thank you again
Regards
Ayesha Fatima
On Fri, 7 Aug 2020, 9:01 pm Matias Machado, <mmachado.pasteur.edu.uy> wrote:
> Dear Ayesha Fatima,
>
> Is there any chance you are generating the file "tleap1.in" in Windows
> and then running in Linux?
>
> My guess is that you may be facing Linux/Windows compatibility issues due
> to the "carriage return", which may be interpreted as an extra argument by
> leap. Hence the error "Improper number of arguments!" despite "not seeing"
> the character in the line...
>
> In Linux you can unmask the issue by executing:
>
> cat -A tleap1.in
>
> then you should see...
>
> source leaprc.protein.ff14SB ^M$
>
> If that's the case, then check this link for possible solutions...
> https://kb.iu.edu/d/acux
>
> Best regards,
>
> Matias
>
> PS: the fact of sending the mail from a Windows 10 computer gave me the
> hint Watson... ;-)
>
> ------------------------------------
> PhD.
> Researcher at Biomolecular Simulations Lab.
> Institut Pasteur de Montevideo | Uruguay
> [http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
> [http://www.sirahff.com]
>
> ----- Mensaje original -----
> De: "Ayesha Fatima" <ayeshafatima.69.gmail.com>
> Para: "AMBER Mailing List" <amber.ambermd.org>
> Enviados: Jueves, 6 de Agosto 2020 13:41:19
> Asunto: [AMBER] tleap.in error
>
> Good morning everyone,
>
>
> I created a tleap.in file and wanted to run it but it keeps giving me the
> syntax error or
>
>
> -I: Adding /mnt/d/amber/amber18/dat/leap/prep to search path.
> -I: Adding /mnt/d/amber/amber18/dat/leap/lib to search path.
> -I: Adding /mnt/d/amber/amber18/dat/leap/parm to search path.
> -I: Adding /mnt/d/amber/amber18/dat/leap/cmd to search path.
> -s: Ignoring startup file: leaprc
> -f: Source tleap1.in.
>
> Welcome to LEaP!
> Sourcing: ./tleap1.in
>
> /mnt/d/amber/amber18/bin/teLeap: Fatal Error!
> source: Improper number of arguments!
> usage: source <filename>
>
>
>
> my file has the following entries
>
> .................
>
> source leaprc.protein.ff14SB
> source leaprc.gaff2
> source leaprc.water.tip3p
> loadamberparams frcmod.ionsjc_tip3p
> set default PBradii mbondi3
> rec=loadpdb rec.pdb
> loadamberparams bras.frcmod
> lig=loadmol2 bras.mol2
> gascomplex= combine {rec lig}
> savepdb gascomplex bras.complex.pdb
> saveamberparm gascomplex bras.gas.complex.prmtop bras.gas.complex.rst7
> saveamberparm rec bras.gas.receptor.prmtop bras.gas.receptor.rst7
>
> ..........................
>
> i used the command
>
>
> tleap -f tleap1.in
>
>
> Am i doing anything wrong?
>
>
>
> Thank you for your guidance
>
>
> Regards
>
> Ayesha
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows
> 10
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>
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Received on Fri Aug 07 2020 - 06:30:04 PDT
