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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