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

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Thu Jul 02 2009 - 19:09:23 CDT

Dear Emilia,

Please keep the discussion in the mailing list. You forgot to add
comments on the following lines:

ATOM HD1 HP 0.115 / | \
ATOM NE1 NY -0.61 HM1 HM2 HM3

Change them to:

ATOM HD1 HP 0.115 ! / | \
ATOM NE1 NY -0.61 ! HM1 HM2 HM3

Cheers,
Leo

On Thu, Jul 2, 2009 at 7:05 PM, emilia wu<emilia.l.wu_at_gmail.com> wrote:
>
> Hi Leonardo,
>
> Thank you so much for your reply, but I can not see any special character in
> my file.
> the attachment is the modified topology file and the pdb file, could you
> please give me some suggestions, it really
> bothers me for the whole day.
> Thank you!
>
> Emilia
> 2009/7/2 Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu>
>>
>> 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
>
>

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

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