Re: [AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue

From: Elvis Martis <elvis.martis.bcp.edu.in>
Date: Thu, 23 Feb 2017 16:35:11 +0000

HI,
Like David, even I could not reproduce any error and my antechamber and parmchk2 smoothly gave their respective outputs (attached here are the prepin and frcmod file along with the sqm files)
Here are the commands I ran on my machine using AMBERtools15
>> source /share/apps/amber14/amber.sh
>> antechamber -i Ser630_bound.mol2 -fi mol2 -o trial.prepin -fo prepi -s 2 -nc 0 -c bcc
>> parmchk2 -i trial.prepin -f prepi -o trial.frcmod

Hope this helps
    Best Regards



Elvis Martis
Ph.D. Student (Computational Chemistry)
 at Bombay College of Pharmacy


A  Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12




-----Original Message-----
From: Nikolay N. Kuzmich [mailto:nnkuzmich.gmail.com]
Sent: Thursday, February 23, 2017 8:19 PM
To: amber.ambermd.org
Subject: Re: [AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue

Dear David, Elvis and other Amber users,


I have Amber 14 and AmberTools 15 versions. The mol2 file does look okay when I open it with Schrodinger Maestro or GaussView, I mean the correctness of valences and absence of dummy atoms.

The ac file, prepared from the mol2 by antechamber, shows C21 having 4 bonds.

Thank you for recommending to rename atoms, I just saw the similar at the
B5 tutorial (with CA, CB, etc.).

How did I create the prepin file:

I took the pdb file with a modified serine from PDB database, then added hydrogens using pdb4amber and edited the pdb with Schrodinger Maestro to build my own modified residue. I also noticed that pdb4amber tried to assign the wrong protonation state for the sp2-hybrid NH group. The excessive proton was deleted. Then I copied the modified residue, added the absent H atom for N tail and OH group for C-tail and saved it as mol2 file (Schrodinger Maestro).

After that I obtained the corresponding ac file employing antechamber, manually built the mc file after the B5 tutorial. After running prepgen application I obtained the prepin file.

That’s how it was…



Thank you,
Nick



Message: 32
Date: Tue, 21 Feb 2017 09:32:02 -0500
From: David Case <david.case.rutgers.edu>
Subject: Re: [AMBER] Segmentation fault when starting parmchk2 for a
        modified aminoacid residue
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20170221143202.oaw4o3757hzyt65l.scarletmail.rutgers.edu>
Content-Type: text/plain; charset=us-ascii

On Tue, Feb 21, 2017, Nikolay N. Kuzmich wrote:
>
> parmchk2 -i Ser630_bound.prepin -f prepi -o frcmod.adf -a Y -p \
> $AMBERHOME/dat/leap/parm/parm10.dat
>
> And then I got message "Segmentation fault".

Can you post the prepin file you are using? We need this to try to reproduce the problem, which is a necessary first step in looking for a fix.

The term "segmentation fault" is just a generic error message, and doesn't provide any information.

...thx...dac



Message: 37
Date: Tue, 21 Feb 2017 16:21:23 +0000
From: "Elvis Martis" <elvis.martis.bcp.edu.in>
Subject: Re: [AMBER] Segmentation fault when starting parmchk2 for a
        modified aminoacid residue
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <
PN1PR01MB0830FA5656289E7318CA3341A3510.PN1PR01MB0830.INDPRD01.PROD.OUTLOOK.COM
>

Content-Type: text/plain; charset="iso-8859-1"

Firstly, Segmentation fault is a general error message, can you post any log files.
Secondly, can tell us what are trying to simulate (little more details are
needed)

? ? Best Regards



Elvis Martis
Ph.D. Student (Computational Chemistry)
?at?Bombay College of Pharmacy


A??Kalina, Santacruz [E], Mumbai 400098, INDIA W?www.elvismartis.in
Skype.?adrian_elvis12




-----Original Message-----
From: Nikolay N. Kuzmich [mailto:nnkuzmich.gmail.com]
Sent: Tuesday, February 21, 2017 7:34 PM
To: amber.ambermd.org
Subject: [AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue

Dear Amber users,

preparing necessary files for simulation of a protein with modified serine residue, I was checking the presense of parameters via parmchk2 application just as it is described in the "Simulating the Green Fluorescent Protein"
tutorial.

parmchk2 -i Ser630_bound.prepin -f prepi -o frcmod.adf -a Y -p \ $AMBERHOME/dat/leap/parm/parm10.dat

The own generated prepin file was employed.
And then I got message "Segmentation fault".
I have found the similar report about this error in the archive via google but still hardly know what to do.
Is it a problem with my prepin file?

What should I pay attention to in it?
And what can be wrong there?

Thank you in advance,
Nick
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http://lists.ambermd.org/mailman/listinfo/amber





-Original Message-----
From: Nikolay N. Kuzmich [mailto:nnkuzmich.gmail.com]
Sent: Tuesday, February 21, 2017 7:34 PM
To: amber.ambermd.org
Subject: [AMBER] Segmentation fault when starting parmchk2 for a modified aminoacid residue

Dear Amber users,

preparing necessary files for simulation of a protein with modified serine residue, I was checking the presense of parameters via parmchk2 application just as it is described in the "Simulating the Green Fluorescent Protein"
tutorial.

parmchk2 -i Ser630_bound.prepin -f prepi -o frcmod.adf -a Y -p \ $AMBERHOME/dat/leap/parm/parm10.dat

The own generated prepin file was employed.
And then I got message "Segmentation fault".
I have found the similar report about this error in the archive via google but still hardly know what to do.
Is it a problem with my prepin file?

What should I pay attention to in it?
And what can be wrong there?

Thank you in advance,
Nick


------------------------------

Message: 39
Date: Wed, 22 Feb 2017 16:25:20 +0000
From: "Elvis Martis" <elvis.martis.bcp.edu.in>
Subject: Re: [AMBER] Segmentation fault when starting parmchk2 for a
        modified aminoacid residue
To: AMBER Mailing List <amber.ambermd.org>
Message-ID:
        <PN1PR01MB083051173F34165FD11713A7A3500.PN1PR01MB0830.
INDPRD01.PROD.OUTLOOK.COM>

Content-Type: text/plain; charset="iso-8859-1"

Hi
I suspect something wrong in your structure (mol2).
Have you checked if all valencies are satisfied?
Can you rename you atoms CA, C, OG, CB, H to something else,? Because this may clash with the atom names given to proteins. CA = alpha carbon; CB for beta carbon and so on...
? ? Best Regards



Elvis Martis
Ph.D. Student (Computational Chemistry)
?at?Bombay College of Pharmacy



Message: 46
Date: Wed, 22 Feb 2017 14:27:21 -0500
From: David Case <david.case.rutgers.edu>
Subject: Re: [AMBER] Segmentation fault when starting parmchk2 for a
        modified aminoacid residue
To: AMBER Mailing List <amber.ambermd.org>
Message-ID: <20170222192721.kubjaxvoan4dfa2f.scarletmail.rutgers.edu>
Content-Type: text/plain; charset=us-ascii

On Wed, Feb 22, 2017, Nikolay N. Kuzmich wrote:
>
> here's the prepin file:

(Easier for us if you attach such files, since files often get mangled by mail
programs.)

>
> the main chain file:
>
> *HEAD_NAME N33TAIL_NAME CMAIN_CHAIN CAOMIT_NAME HNOMIT_NAME
> O31OMIT_NAME H34PRE_HEAD_TYPE CPOST_TAIL_TYPE NCHARGE 0.0*

Not sure what you be using the above for(?)

> >
> > parmchk2 -i Ser630_bound.prepin -f prepi -o frcmod.adf -a Y -p \
> > $AMBERHOME/dat/leap/parm/parm10.dat
> >
> > And then I got message "Segmentation fault".
>

Doesn't give a segfault for me, although it does complain about the DU atoms, which is a bit strange. But parmchk2 is primarily designed for the gaff force fields, so there might be something related to that. Which version of AmberTools are you using?

I'm not following exactly your workflow here. The mol2 file has a carbon with only three single bonds to it (C21); not sure if that has anything to do with what you see or not. Also, I don't see anything obviously wrong with the prepin file, and I can't reproduce the seg fault. Bottom line is that I'm not able to provide much help here (unless it's just a matter of needing to update to the current version of the codes.)

Can you say more about exactly what you did to create the prepin file?

...dac

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Received on Thu Feb 23 2017 - 09:00:03 PST
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