Re: ERROR! Explicit exclusions or fluctuating charges not supported, atom ignored.

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Thu Jul 02 2009 - 18:55:23 CDT

Hi Emilia,

On Thu, Jul 2, 2009 at 6:35 PM, emilia wu<emilia.l.wu_at_gmail.com> wrote:
> Hi all,
>
> I want to run a md simulation for a small peptide with 13 amino acid, there
> is an unnatural amino acid, just add another CH3 group on the side chain of
> Trp4.
> I modified the topology file of charmm top_all27_prot_na.rtf, and add this
> part. the red one is modified part from TRP.
> RESI W4M          0.00
> GROUP
> ATOM N    NH1    -0.47  !     |                  HE3
> ATOM HN   H       0.31  !  HN-N                   |
> ATOM CA   CT1     0.07  !     |   HB1            CE3
> ATOM HA   HB      0.09  !     |   |             /  \\
> GROUP                   !  HA-CA--CB---CG-----CD2   CZ3-HZ3
> ATOM CB   CT2    -0.18  !     |   |    ||     ||     |
> ATOM HB1  HA      0.09  !     |   HB2  CD1    CE2   CH2-HH2
> ATOM HB2  HA      0.09  !   O=C       /   \   / \  //
> GROUP                   !     |     HD1    NE1   CZ2
> ATOM CG   CY     -0.03  !                   |     |
> ATOM CD1  CA      0.035 !                  CM1   HZ2
> ATOM HD1  HP      0.115                  /  |  \
> ATOM NE1  NY     -0.61                 HM1 HM2 HM3
> ATOM CM1  CT3     0.11
> ATOM HM1  HA      0.09
> ATOM HM2  HA      0.09
> ATOM HM3  HA      0.09
> ATOM CE2  CPT     0.13
> ATOM CD2  CPT    -0.02
> GROUP
> ATOM CE3  CA     -0.115
> ATOM HE3  HP      0.115
> GROUP
> ATOM CZ3  CA     -0.115
> ATOM HZ3  HP      0.115
> GROUP
> ATOM CZ2  CA     -0.115
> ATOM HZ2  HP      0.115
> GROUP
> ATOM CH2  CA     -0.115
> ATOM HH2  HP      0.115
> GROUP
> ATOM C    C       0.51
> ATOM O    O      -0.51
> BOND CB  CA   CG  CB   CD2 CG   NE1 CD1
> BOND CZ2 CE2
> BOND N   HN   N   CA     C   CA   C   +N
> BOND CZ3 CH2  CD2 CE3  NE1 CE2  CA  HA   CB  HB1
> BOND CB  HB2  CD1 HD1  NE1 CM1  CE3 HE3  CZ2 HZ2
> BOND CZ3 HZ3  CH2 HH2
> BOND CM1 HM1  CM1 HM2  CM1 HM3
> DOUBLE  O   C   CD1 CG   CE2 CD2  CZ3 CE3  CH2 CZ2
> IMPR N -C CA HN  C CA +N O
> DONOR HN N
> ACCEPTOR O C
>
> After I modified the topology file, I use psfgen to read the pdb file, but
> it gave this message:
>
> ERROR!  Explicit exclusions or fluctuating charges not supported, atom
> ignored.
> ERROR!  Explicit exclusions or fluctuating charges not supported, atom
> ignored.
>
> what does this mean, what should I do?

psfgen is failing when trying to read some ATOM statement:

    else if ( ! strncmp("ATOM",tok[0],4) ) {
      debug_msg("Recognized atom statement.");
      if ( ntok < 4 ) {
        print_msg(v,"ERROR! Failed to parse atom statement.");
      } else if ( ntok > 4 ) {
        print_msg(v,"ERROR! Explicit exclusions or fluctuating
charges not supported, atom ignored.");
      } else {
        s1 = parse_atom(tok[1],&i1,&j1);
        if ( topo_defs_atom(defs,0,0, s1,i1,j1,tok[2],atof(tok[3])) ) {
          print_msg(v,"ERROR! Failed to parse atom statement.");
        }
      }
    }

It looks like it is recognizing more than 4 tokens. Make sure you
don't have any special characters on the lines you modified.

Cheers,
Leo

> I notice even if I did not read this unnatural amino acid, the error is
> still there  only if the topology file was changed.
>
> Thanks in advance!
>
> Emilia
>
>
>
>

-- 
Leonardo Trabuco, Ph.D. candidate
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign

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