[gmx-users] Diagnosing + system blowing up

Shima Arasteh shima_arasteh2001 at yahoo.com
Sun Jul 29 14:39:52 CEST 2012


So as I got the atomtypes have problem!
OK, I will do some exercise with charmm36 and acetyl.
Anyway, thanks for all your suggestions. However now my dead is going dizzy :)


Sincerely,
Shima


----- Original Message -----
From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Sunday, July 29, 2012 5:01 PM
Subject: Re: [gmx-users] Diagnosing + system blowing up

On 29/07/2012 10:17 PM, Shima Arasteh wrote:
>
>
>
> Pleas don't shrug!
> Sorry :-(
> I attach the top file generated by pdb2gmx and this is what I see in terminal:
> Processing chain 1 (177 atoms, 24 residues)
> Identified residue FVAL1 as a starting terminus.
> Identified residue GLY24 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Select start terminus type for FVAL-1
>   0: NH3+
>   1: NH2
>   2: None
> 2
> Start terminus FVAL-1: None
> Select end terminus type for GLY-24
>   0: COO-
>   1: COOH
>   2: CT2
>   3: CT3
>   4: None
> 0
> End terminus GLY-24: COO-
> Opening force field file ./charmm36-modified.ff/aminoacids.arn
> Opening force field file ./charmm36-modified.ff/dna.arn
> Opening force field file ./charmm36-modified.ff/rna.arn
> Checking for duplicate atoms....
> Now there are 24 residues with 360 atoms
> Making bonds...
> Number of bonds was 362, now 362
> Generating angles, dihedrals and pairs...
> Before cleaning: 925 pairs
> Before cleaning: 930 dihedrals
> Keeping all generated dihedrals
> Making cmap torsions...There are   22 cmap torsion pairs
> There are  930 dihedrals,   49 impropers,  644 angles
>             916 pairs,      362 bonds and     0 virtual sites
> Total mass 2510.906 a.m.u.
> Total charge 1.000 e
> Writing topology
>
>  
> Then eneter commands:
> # editconf -f monomer.gro -o monomer_newbox.gro -c -d 1.0 -bt cubic
> # genbox -cp monomer_newbox.gro -cs spc216.gro -o monomer_solv.gro -p topol.top
> # grompp -f ions.mdp -c monomer_solv.gro -p topol.top -o ions.tpr
>
> This is what I get from grompp:
>
>    
>
> Generated 21528 of the 21528 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 1
> Generated 18355 of the 21528 1-4 parameter combinations
>
> ERROR 1 [file topol.top, line 414]:
>    No default Bond types
>      1     2     1
>
>
> ERROR 2 [file topol.top, line 1698]:
>    No default U-B types
>      2     1     3     5
>
>
> ERROR 3 [file topol.top, line 1699]:
>    No default U-B types
>      2     1     4     5
>
>
> ERROR 4 [file topol.top, line 2345]:
>    No default Proper Dih. types
>      2     1     4     5     9
>
>
> ERROR 5 [file topol.top, line 2346]:
>    No default Proper Dih. types
>      2     1     4     6     9
>
>
> ERROR 6 [file topol.top, line 3278]:
>    No default Improper Dih. types
>      1     4     3     2     2

So you need to deal with all of this. Presumably you are not using the 
right atom type for formyl C,H,O atoms, or there aren't such, or 
something. Those indices above are relative to the output topol.top, not 
the .rtp. You need to do some homework on what CHARMM36 has in it... 
scan atomtypes.atp for a start. Or use acetyl like a normal person. :-)

Mark

>
> Excluding 3 bonded neighbours molecule type 'Protein'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> NOTE 1 [file topol.top, line 3378]:
>    System has non-zero total charge: 1.000000
>    Total charge should normally be an integer. See
>    http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>    for discussion on how close it should be to an integer.
>    
>
>
>
> There was 1 note
>
> -------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/grompp.c, line: 1372
>
> Fatal error:
> There were 6 errors in input file(s)
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
>
> This is all I got.
> I couldn't attach the .top file, it was too big.
>
> Sincerely,
> Shima
>
>
> ________________________________
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Sent: Sunday, July 29, 2012 4:07 PM
> Subject: Re: [gmx-users] Diagnosing + system blowing up
>
> On 29/07/2012 9:31 PM, Shima Arasteh wrote:
>> grompp warns me for some bonds and dihedrals ( no default ).
>> Ignoring such warnings gives me the same error as before ( some interactions seems to be assigned multiple times)
>>
>> Maybe I didn't modify the .rtp file correctly!
> Shrug... if you won't copy and paste your output you can't be helped. As
> I've said, ignoring warnings is asking for trouble unless you really
> know why you can do it. But I'm going to stop repeating myself.
>
> Mark
>
>>    
>> Sincerely,
>> Shima
>>
>>
>> ----- Original Message -----
>> From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Cc:
>> Sent: Sunday, July 29, 2012 3:39 PM
>> Subject: Re: [gmx-users] Diagnosing + system blowing up
>>
>> Thanks dear Mark.
>> I don't use ignh. This is the command of pdb2gmx which I enter:
>> pdb2gmx -f monomer.pdb -o monomer.gro -water tip3p -ter
>>
>>
>> grompp does not give me the warning of that the atom names in the topology and the coordinate file don't match, instead it gives me that there are no default bonds/dihedrals ( Now I can see atom 18 in all lines which is defined by grompp)
>>
>> So, change this line of .hdb
>> 1    1    H1    C    N    O
>> to
>>
>> 1    1    H1    CN    N    ON
>> N  is the N of Valine and ON is the O of formyl.
>>
>> I'll check it out right now.
>>
>>
>>
>>
>>    
>> Sincerely,
>> Shima
>>
>>
>> ----- Original Message -----
>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Cc:
>> Sent: Sunday, July 29, 2012 2:48 PM
>> Subject: Re: [gmx-users] Diagnosing + system blowing up
>>
>> On 29/07/2012 7:55 PM, Shima Arasteh wrote:
>>> I listened to you absolutely and didn't proceed any other way!  What I created in .rtp file for  FVAL ( like what you described sometime ago), is  as below:
>>> First of all added the FVAL to residuetyes.dat.
>>>
>>> Then added to .rtp file:
>>>
>>> [ FVAL ]
>>>       [ atoms ]
>>>          CN    C    0.357    0
>>>          ON    O    -0.51    1
>>>          H1    HA    0.100    2
>>>          N    NH1    -0.423    3
>>>          HN    H    0.333    4
>>>          CA    CT1    0.034    5
>>>          HA    HB    0.09    6
>>>          CB    CT1    -0.093    7
>>>          HB    HA    0.09    8
>>>          CG1    CT3    -0.268    9
>>>          HG11    HA    0.09    10
>>>          HG12    HA    0.09    11
>>>          HG13    HA    0.09    12
>>>          CG2    CT3    -0.268    13
>>>          HG21    HA    0.09    14
>>>          HG22    HA    0.09    15
>>>          HG23    HA    0.09    16
>>>          C    C    0.528    17
>>>          O    O    -0.510    18
>>>       [ bonds ]
>>>          CN    H1
>>>          CN    ON
>>>          CN    N
>>>          N    H
>> You don't have an atom named H, but maybe this is succeeding because I
>> patched pdb2gmx to accept HN or H in some cases...
>>
>>>          CA    N
>>>          CA    HA
>>>          CA    C
>>>          C    O
>>>          CA    CB
>>>          CB    HB
>>>          CB    CG1
>>>          CB    CG2
>>>          CG2    HG21
>>>          CG2    HG22
>>>          CG2    HG23
>>>          CG1    HG11
>>>          CG1    HG12
>>>          CG1    HG13
>>>          
>>>       [ impropers ]
>>>        CN     N    ON    H1
>>>
>>> And at last adding H atoms to .hdb:
>>> 1    1    H1    C    N    O
>> Why are you adding your formyl hydrogen to the carbon named C, which is
>> part of the peptide bond after valine? Here's your problem. You're
>> presumably using pdb2gmx -ignh (but you should be copying your pdb2gmx
>> command into your email so we're not wasting time guessing...) H is
>> being added back in as atom 1, and so you have a bond from the new atom
>> 1 to atom 18 (that carbon). Probably, that's being matched to the
>> coordinates of the original CN atom (leading to the long bond warning,
>> and then to blowing up), grompp is warning you that the atom names in
>> the topology and the coordinate file don't match, and you've been
>> ignoring that warning too. There's a reason all the
>> http://www.gromacs.org/Support page asks for copied and pasted input and
>> output, evidence of modified files, and for you to have read all the
>> output. I suspect there's been a lot of time wasted on this thread ;-)
>>
>> Mark
>>
>>> 1    1    HN    N    C    CA
>>> 1    5    HA    CA    N    C    CB
>>> 1    5    HB    CB    CA    CG1    CG2
>>> 3    4    HG1    CG1    CB    CA
>>> 3    4    HG2    CG2    CB    CA
>>>
>>>
>>> I tried to follow your suggestion exactly! Believe me! :-)
>>>
>>> Sincerely,
>>> Shima
>>>
>>>
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