This is really strange.
> this issue hit me just two days ago.
So it has worked before?
What is stranger in retrospect is that you suggested you are able to run antechamber on both systems without generating any error. This means that you already have (almost) the same flags (-i, -o -f(i)) working and no characters running pamrchk2 have not already been used running antechamber, so that blows a big hole in my theory.
The OS "should not" make a difference as you are not running the commands locally but on the server. My guess whas that there could be a difference in what is being sent to the server, that you were not executing the command you thought you where from the linux machine. If it has worked before then it is even more surprising.
What happens if you try a different format (prepi), well from the machine where it is not working at a later point.
Best regards
// Gustaf
> On 10 Sep 2020, at 09:09, Lod King <lodking407.gmail.com> wrote:
>
> "So you are technically working on the cluster when running the commands,
> ssh connected from a linux station terminal and from a mac terminal?"
> yes!
>
> "Connecting over SSH from your linux machine produces the error and
> connecting from mac does not?"
> yes!
>
> "Are there any other differences in the setup? "
> No, I worked with the same folder with those AN TECH~~~~ files and the
> prepc file.
> All I did was ssh to the cluster via both my mac and my linux, and hit $
> parmck2 ******** on my mac terminal when I got the flags indication errors
> in my linux, frcmod file was generated.
>
> Are the systems configured with different languages, are there any other
> particular settings changed in the SSH connection protocol?
> Well, Linux is Ubuntu os, and MAC is mac os. but I logged in to cluster via
> terminal using the same account.
> I don't think the setting of SSH connection protocol has changed and I just
> did that a few days ago, and this issue hit me just two days ago.
>
> from my mac, I got the following. As to test in my Linux, I have to get
> into the lab when I have a chance.
>
> [cluster-gpu0 ~]$ history | grep antechamber
>
> 567 antechamber -i 3m2.pdb -fi pdb -o 3m2.prepc -fo prepc -nc -0 -c bcc
> -s 2 -at gaff2
>
> 569 antechamber -i 3m2.pdb -fi pdb -o 3m2.prepc -fo prepc -nc -0 -c bcc
> -s 2 -at gaff2
>
> 571 antechamber -i 3m2.pdb -fi pdb -o 3m2.prepc -fo prepc -nc -0 -c bcc
> -s 2 -at gaff2
>
> 591 antechamber -i 3m3.pdb -fi pdb -o 3m3.prepc -fo prepc -nc -0 -c bcc
> -s 2 -at gaff2
>
> 593 antechamber -i 3m3.pdb -fi pdb -o 3m3.prepc -fo prepc -nc -0 -c bcc
> -s 2 -at gaff2
>
> 963 antechamber -i 4m1.pdb -fi pdb -o 4m1.prepc -fo prepc -nc -0 -c bcc
> -s 2 -at gaff2
>
> [cluster-gpu0 ~]$ history | grep parmchk2
>
> 543 parmchk2 -i 3m1.prepc -f prepc -o 3m1.frcmod -s 2 -a Y
>
> 547 parmchk2 -i 3m1.prepc -f prepc -o 3m1.frcmod -a Y
>
> 574 parmchk2 -i 3m2.prepc -f prepc -o 3m2.frcmod -a Y
>
> 594 parmchk2 -i 3m3.prepc -f prepc -o 3m3.frcmod -a Y
>
> 964 parmchk2 -i 4m1.prepc -f prepc -o 4m1.frcmod -a Y
>
>
> So all in all, I could not think of any other reasons besides the OS.
>
> On Wed, Sep 9, 2020 at 11:50 PM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
>> So you are technically working on the cluster when running the commands,
>> ssh connected from a linux station terminal and from a mac terminal?
>>
>> Connecting over SSH from your linux machine produces the error and
>> connecting from mac does not?
>>
>> This is somewhat surprising as you are technically working on the server
>> and not on your local workstation. Are there any other differences in the
>> setup? Are the systems configured with different languages, are there any
>> other particular settings changed in the SSH connection protocol?
>>
>> As you are running the commands on the server, they should all be stored
>> in history. If you login from your mac, where the command(s) work, and try
>> to execute the “non-working” command previously executed from the Linux
>> machine, does it work?
>>
>> $ history | grep antechamber
>>
>> In the printout you should be able to rather quickly compare if there are
>> any visual differences and copy and execute one of the older commands which
>> failed to execute to see if it works now.
>>
>> I am not a an expert in any way or form though just from the sound of it,
>> my guess would be a language/locale or some other “format” problem.
>>
>> Best regards
>> // Gustaf
>>
>>> On 9 Sep 2020, at 16:12, Lod King <lodking407.gmail.com> wrote:
>>>
>>> Hello, Gustaf
>>>
>>> If dropping "-a Y", I would get the printout with partial info missed",
>> not
>>> sure why.
>>>
>>> In addition, all work was done in my Linux station, which I ssh to work
>> at
>>> our supercomputer station.
>>>
>>> and Then, I switched to my mac and ssh via terminal to work at
>>> supercomputer, everything is normal, I got the prepc and frcmod of I
>> need,
>>> very confused.
>>>
>>> On Wed, Sep 9, 2020 at 12:20 AM Gustaf Olsson <gustaf.olsson.lnu.se>
>> wrote:
>>>
>>>> If I run the same command as you, having none of the files, I get the
>>>> expected error
>>>>
>>>> Cannot open file (ligand.prepc) with mode (r).
>>>> No such file or directory
>>>>
>>>> The printout presented is what I receive when running "parmchk2” without
>>>> any input or options/flags. This would suggest an incorrect command. I
>>>> might be going blind though I cannot se any obvious errors with the
>>>> supplied commands.
>>>>
>>>> The -i, -f and -o flags are, as far as I know, the only required flags.
>>>> What happens if you drop the “-a Y”?
>>>>
>>>> Best regards
>>>> // Gustaf
>>>>
>>>>> On 9 Sep 2020, at 03:25, Lod King <lodking407.gmail.com> wrote:
>>>>>
>>>>> Hello AMBER
>>>>>
>>>>> I used to use the following commands to generate prepc and frcmod
>> files.
>>>>>
>>>>> $ antechamber -i ligand.pdb -fi pdb -o ligand.prepc -fo prepc -nc -2 -c
>>>> bcc
>>>>> -s 2 -at gaff2
>>>>>
>>>>> and parmchk for the frcmod file:
>>>>>
>>>>> $ parmchk2 -i ligand.prepc -f prepc -o ligand.frcmod -a Y
>>>>>
>>>>> now I am able to generate ligand.prepc, but when hitting parmchk2, it
>>>>> prompts me to
>>>>>
>>>>> $ parmchk2 -i ligand.prepc -f prepc -o ligand.frcmod -a Y
>>>>> Usage: parmchk2 -i input file name
>>>>> -o frcmod file name
>>>>> -f input file format (prepi, prepc, ac, mol2)
>>>>> -s ff parm set, it is suppressed by "-p" option
>>>>> 1: gaff (the default)
>>>>> 2: gaff2
>>>>> -p parmfile
>>>>> -pf parmfile format
>>>>> 1: for amber FF data file (the default)
>>>>> 2: for additional force field parameter file
>>>>> -c atom type corresponding score file, default is
>>>>> PARMCHK.DAT
>>>>> -a print out all force field parameters including those
>>>> in
>>>>> the parmfile
>>>>> can be 'Y' (yes) or 'N' (no) default is 'N'
>>>>> -w print out parameters that matching improper dihedral
>>>>> parameters
>>>>> that contain 'X' in the force field parameter file,
>>>> can
>>>>> be 'Y' (yes)
>>>>> or 'N' (no), default is 'Y'
>>>>>
>>>>> Did I miss any flags?
>>>>> _______________________________________________
>>>>> 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
>>
> _______________________________________________
> 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 Thu Sep 10 2020 - 01:00:02 PDT
