<P>
Sir,<BR>
I have a protein transferrinthat contains a Fe and a CO3 hetero molecule. I used the ffG43a1 force field. When i ran pdb2gmx i got an ERROR saying the CO3 residue was not found in the database. I tried to add the molecule to the datadase i got the itp file from PRODRG2 server :<BR>
<BR>
; Questions/comments to dava@davapc1.bioch.dundee.ac.uk<BR>
; <BR>
; When using this software in a publication, cite:<BR>
; A. W. Schuettelkopf and D. M. F. van Aalten (2004).<BR>
; PRODRG - a tool for high-throughput crystallography<BR>
; of protein-ligand complexes.<BR>
; Acta Crystallogr. D60, 1355--1363.<BR>
; <BR>
; <BR>
<BR>
[ moleculetype ]<BR>
; Name nrexcl<BR>
CO3 3<BR>
<BR>
[ atoms ]<BR>
; nr type resnr resid atom cgnr charge mass<BR>
1 OM 1 CO3 OAA 1 -0.221 15.9994<BR>
2 C 1 CO3 CAC 1 0.494 12.0110<BR>
3 OM 1 CO3 OAB 1 -0.221 15.9994<BR>
4 OM 1 CO3 OAD 1 -0.052 15.9994<BR>
<BR>
[ bonds ]<BR>
; ai aj fu c0, c1, ...<BR>
1 2 1 0.125 418400.0 0.125 418400.0 ; OAA CAC<BR>
2 3 1 0.125 418400.0 0.125 418400.0 ; CAC OAB<BR>
2 4 1 0.125 418400.0 0.125 418400.0 ; CAC OAD<BR>
<BR>
[ pairs ]<BR>
; ai aj fu c0, c1, ...<BR>
<BR>
[ angles ]<BR>
; ai aj ak fu c0, c1, ...<BR>
1 2 3 1 126.0 502.1 126.0 502.1 ; OAA CAC OAB<BR>
1 2 4 1 126.0 502.1 126.0 502.1 ; OAA CAC OAD<BR>
3 2 4 1 126.0 502.1 126.0 502.1 ; OAB CAC OAD<BR>
<BR>
[ dihedrals ]<BR>
; ai aj ak al fu c0, c1, m, ...<BR>
2 4 3 1 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CAC OAD OAB OAA<BR>
<BR>
and then i tried to update the ff<***>.rtp file by adding the following lines to the last of the .rtp file <BR>
[CO3]<BR>
[atoms]<BR>
OAA OM -0.221 0<BR>
CAC C 0.494 1<BR>
OAB OM -0.221 0<BR>
OAD OM -0.052 2<BR>
I obtained the details from the .itp file from PRODRG2 server<BR>
but still i am not able to run pdb2gmx the error is that :<BR>
"Atom C in residue CO3 330 not found in rtp entry with 4 atoms while sorting atoms "<BR>
<BR>
I dont know how to proceed further. <BR>
please guide me where i went wrong
</P>
<br><br>
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