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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