[gmx-users] Fatal error: No atoms found in .rtp file in residue pairs

Shima Arasteh shima_arasteh2001 at yahoo.com
Mon May 14 10:52:43 CEST 2012


Thanks for your suggestions.
This is the .itp file got from the SwissParam.
[ atoms ] 
; nr type resnr resid atom cgnr charge mass 
  1 C=O  1  LIG C       1  0.5700  12.0110 
   2 O=C  1  LIG O       2 -0.5700  15.9994 
   3 NC=O 1  LIG N       3 -0.7301  14.0067 
   4 CR   1  LIG CA      4  0.1941  12.0110 
   5 CO2M 1  LIG C1      5  0.9060  12.0110 
   6 O2CM 1  LIG O1      6 -0.9000  15.9994 
   7 CR   1  LIG CB      7  0.0000  12.0110 
   8 CR   1  LIG CG1     8  0.0000  12.0110 
   9 CR   1  LIG CG2     9  0.0000  12.0110 
  10 O2CM 1  LIG OXT    10 -0.9000  15.9994 
  11 HCMM 1  LIG H      11  0.0600   1.0079 
  12 HNCO 1  LIG H1     12  0.3700   1.0079 
  13 HCMM 1  LIG HA     13  0.0000   1.0079 
  14 HCMM 1  LIG HB     14  0.0000   1.0079 
  15 HCMM 1  LIG HG11   15  0.0000   1.0079 
  16 HCMM 1  LIG HG12   16  0.0000   1.0079 
  17 HCMM 1  LIG HG13   17  0.0000   1.0079 
  18 HCMM 1  LIG HG21   18  0.0000   1.0079 
  19 HCMM 1  LIG HG22   19  0.0000   1.0079 
  20 HCMM 1  LIG HG23   20  0.0000   1.0079 

Now I made this .rtp file as below:
 [ For ]
 [ atoms ]
;      name    type     charge   chargegroup
        C       CTL1     0.5700        0
        O       O           -0.5700        0
        H       HC         0.06              0
 [angles ]
  ai    aj    ak   
  O     C     +N 
  O     C      H
  O    
 C     +N

 [ bonds ]
     C      O    
     C     +N
     C      H
 
 [ dihedrals ]
  O     C   +N   +CA 
  H     C   +N   +H 
  H     C   +N   +H

You
 know, actually I want to get a correct .itp file to use it later the 
paramers later if it is needed. would you suggest me about this file?

Sincerely,
Shima
 
Sincerely,
Shima


________________________________
 From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Monday, May 14, 2012 12:42 PM
Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs
 

On 14/05/2012 6:00 PM, Shima Arasteh wrote: 
Thanks for your suggestions.
>Now, I think that it's better to add the N atom of next residue  to the .pdb file and then add hydrogen atoms to its .mol2 format. Because when I open formyl.pdb in  chimera software and add hydrogens to it, it becomes an formaldehyde and then I get the a wrong parameters in .itp file by using SwissParam. So I didn't remove the N  atom which connects to the C of formyl. Now I got this .itp file:
> 
>
>; nr type resnr resid atom cgnr charge mass 
>   1 CR   1  LIG C       1  0.5500  12.0110 
>   2 OR   1  LIG O       2 -0.6800  15.9994 
>   3 HCMM 1  LIG H4      3  0.0000   1.0079 
>   4 HCMM 1  LIG H6      4  0.0000   1.0079 
>   5 HOR  1  LIG H8      5  0.4000   1.0079 
>   6 NR   1  LIG N       6 -0.9900  14.0067 
>   7 HNR  1  LIG H2      7  0.3600   1.0079 
>   8 HNR  1  LIG H1      8  0.3600   1.0079 
>
>
>
>Would this file work probably? I mean can  I get the correct parameters?
Since you can't have a double bond with that many bonded hydrogen
    atoms present, no.

Like Justin has suggested, one approach is to take the whole residue
    adjacent to formyl and parameterise all of it. Another would be to
    take the acetyl group for that force field and assign the total
    charge of the methyl group to the hydrogen of your formyl - but this
    has obvious shortcomings.



>
>The .rtp file which I arranged, is as below:
>[ For ]
> [ atoms ]
>;      name    type     charge   chargegroup
>        C       CTL1     0.5500       0
>        O       O       -0.6800       0
>        H       HC       0.1300      0
> [angles ]
>  ai    aj    ak   
>  O     C     +N 
>  O     C      H
>  H     C     +N
>
> [ bonds ]
>     C      O    
>     C     +N
>     C      H
> 
> [ dihedrals ]
>  O     C   +N   +CA 
>  H     C   +N   +H
> H      C    +N    +H
>
>
>Would it be correct? I got the charge of H atom by assuming the total charge of formyl is zero.
Only if you think the carbonyl group forming an amide bond consists
    only of atoms with equivalent electronegativity. Any model that does
    not have partial negative charge on the oxygen will be not worth the
    time to write down.

Mark


>
>
>
>
>
>
>
>
>
>Sincerely,
>Shima
>
>
>________________________________
> From: Justin A. Lemkul <jalemkul at vt.edu>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
>Sent: Sunday, May 13, 2012 9:40 PM
>Subject: Re: [gmx-users] Fatal error: No atoms found in .rtp file in residue pairs
> 
>
>
>On 5/13/12 12:42 PM, Shima Arasteh wrote:
>> OK, so I entered the H atom corresponding to the
            structure and then changed the
>> file as below,
>>
>> [ For ]
>> [ atoms ]
>> ; name type charge charge group
>> C CTL1 0.5700 0
>> O O -0.5700 0
>> H HC 0.00 0
>>
>
>I find it highly unlikely that a zero charge should be
            assigned to this proton. 
>  The .itp file you posted before from SwissParam was for
            formaldehyde, which 
>suggests to me you haven't properly parameterized the
            species you're looking for 
>and now you're trying to hack something together.  Don't try
            to do that; your 
>parameters will be junk.  Parameterize the right species
            once and proceed from 
>there.
>
>> [angles ]
>> ai aj ak
>> O C +N
>> O C H
>>
>> [ bonds ]
>> C O
>> C +N
>> C H
>>
>> [ dihedrals ]
>> O C +N +CA
>> H C +N +H
>>
>
>There are other possible dihedrals here.
>
>-Justin
>
>>
>>
>>
--------------------------------------------------------------------------------
>> *From:* Justin A. Lemkul <jalemkul at vt.edu>
>> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
>> *Sent:* Sunday, May 13, 2012 8:36 PM
>> *Subject:* Re: [gmx-users] Fatal error: No atoms found
            in .rtp file in residue pairs
>>
>>
>>
>> On 5/13/12 11:43 AM, Shima Arasteh wrote:
>>  > Again thanks for all your replies.
>>  > As I got through your advices, I found that the
            atoms contribute in making bonds
>>  > and angles in a residue , or make dihedrals in a
            residue ( or with atoms in next
>>  > ones) plus the charge of a the residue should be
            defined properly in .rtp files
>>  > to define the new residue in aminoacid.rtp file
            of CHARMM36 force field.
>>  > So I arranged this lines to define formyl in .rtp
            file. And I got the topology.
>>  > But there are some questions for me here:
>>  >
>>  > 1. How can I be sure the formyl which I defined
            is correct? Is getting the
>>  > topology is enough to be sure of the correct
            output?
>>  >
>>
>> It is incorrect. As I said before, a formyl group is an
            aldehyde and has an H
>> atom attached to C, e.g. -CH(=O). At present, you are
            defining a -C=O group
>> with an incomplete carbon valence.
>>
>> http://en.wikipedia.org/wiki/Aldehyde
>>
>>  > The .rtp file for formyl is as below:
>>  > [ For ]
>>  > [ atoms ]
>>  > ; name type charge chargegroup
>>  > C CTL1 0.5700 0
>>  > O O -0.5700 0
>>  > [angles ]
>>  > ai aj ak
>>  > O C +N
>>  > [ bonds ]
>>  > C O
>>  > C +N
>>  >
>>  > [ dihedrals ]
>>  > O C +N +CA
>>  >
>>
>> Aside from the missing atom (and resulting missing
            bonds, angles, and dihedral),
>> the format of this entry is OK.
>>
>>  > 2. There are lots of numbers in .itp file which I
            got through the swissparam.
>>  > But I think the charge of atoms may be useful in
            this file and also I can just
>>  > find the atoms contribute in bonds and angles
            and.... . Am I right? Or I may get
>>  > some other useful information which I can get
            through the files of swissparam?
>>  >
>>
>> If the existing bonded parameters for each interaction
            type (in ffbonded.itp)
>> are sufficient for defining these interactions, then
            you can omit the content of
>> the .itp file you've been using in the .rtp entry and
            rely on the force field to
>> look up those values. There may be some interactions
            that are not in agreement
>> (or do not exist), in which case you need to either
            define these parameters in
>> the .rtp entry itself or in ffbonded.itp so that they
            will be detected by grompp
>> later.
>>
>> -Justin
>>
>>  > Thanks in advance, and sorry for disturbing you
            friends.
>>  > Shima
>>  >
>>  >
--------------------------------------------------------------------------------
> 
            list. Use the
>>  > www interface or send it to gmx-users-request at gromacs.org
>> <mailto:gmx-users-request at gromacs.org>
>
>
>
>
>

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