<P>HI all:</P>
<P>I want to run a simulation with heme group(cytochrome p450). i have made a 3-d structure model for a cytochrome p450 .<FONT face="新宋体"><TT>I use the ffG43a1 force field,someone told me that i need both suitable parameters for your desired force field, and then </TT><TT>to construct a correct topology.</TT></FONT> <FONT face="新宋体">I read lots of papers,but most of them used amber force field.</FONT>Befor runing the gromacs molecular simulation,i define the heme group as a new residue in the .rtp files,following the required formats(atoms,bonds exclusions,angles,impropers,dihedrals)and then define a new FE-S bong.</P>
<P>i run the simulation like this:</P>
<P>pdb2gmx -ignh -ff G43a1 -f CYP2W1_CYSHEME.pdb -o new1.pdb -p new1.top -water spce <BR>editconf -bt cubic -f new1.pdb -o new2.pdb -d 0.9 <BR>genbox -cp new2.pdb -cs spc216.gro -o new3.pdb -p new1.top <BR>grompp -f em.mdp -c new3.pdb -p new1.top -o em.tpr <BR>genion -s em.tpr -o new5.pdb -nname CL- -nn 1 -g ion.log; Edit top file, delette em.tpr <BR>grompp -f em.mdp -c new5.pdb -p new1.top -o em.tpr <BR>mdrun -s em.tpr -o em.trr -c new7.pdb -g em.log -e em.edr <BR>grompp -f pr.mdp -c new7.pdb -p new1.top -o pr.tpr <BR>mdrun -s pr.tpr -o pr.trr -c new9.mdp -e pr.edr -g pr.log </P><PRE style="MARGIN: 0em"></PRE>
<P><FONT face="新宋体"><TT> </TT></FONT><FONT face="新宋体"><TT>1 i run <FONT face="宋体">pdb2gmx and get the new1.pdb ,when checking the pdb with accelrys ds visualizer or sybyl,the atom FE was recognized as F (Fluorine)and the pdb miss the bonds between FE-S &FE-N,i add or delete a blank space befor or after the FE in the pdb file,it was read as iron(FE) again but still missing;when checking the .top file,there was a FE (both atom name and type)and formed the FE-S & FE-N bonds.</FONT></TT></FONT></P>
<P><TT><FONT face="宋体">if i ignore the above things,go on the command ,when runing the em.mdp there is a tip that Steepest Descents failed converged to Fmax < 1000 in 5001 steps.when run the pr.tpr,a error emerged as segment fatal error。</FONT></TT></P>
<P><FONT face="新宋体"><TT>2 <FONT face="新宋体">someone told me that i need both suitable parameters for your desired force field, and then <TT>to construct a correct topology.</TT></FONT><FONT face="宋体"> </FONT><FONT face="新宋体">I read lots of papers,but most of them used amber force field.</FONT></TT></FONT><FONT face="新宋体"><TT>Does anyone known a paper with a gromacs <FONT face="新宋体">force field for HEME group?</FONT></TT></FONT></P>
<P><TT><FONT face="新宋体"><STRONG>please help me how handle those problems,how can i go on the simulation?</STRONG></FONT></TT></P>
<P><TT><FONT face="新宋体">the HEME-cysteine parameter in the rtp files,define themas a new residue.(is there any problems?)</FONT></TT></P>
<P><TT>[ HEME ] <BR> [ atoms ] <BR> N N -0.28000 0 <BR> H H 0.28000 0 <BR> CA CH1 0.00000 1 <BR> CB CH2 -0.10000 2 <BR> SG S -0.40000 2 <BR> C C 0.38000 3 <BR> O O -0.38000 3 <BR> FE FE 0.84700 4 <BR> NA NR -0.37000 4 <BR> NB NR -0.42300 4 <BR> NC NR -0.50400 4 <BR>........<BR> [ bonds ] <BR> N H gb_2 <BR> N CA gb_20 <BR> CA C gb_26 <BR> C O gb_4 <BR> C +N gb_9 <BR> CA CB gb_26 <BR> CB SG gb_30 <BR> SG FE gb_48 <BR> FE NA gb_34 <BR> FE NB gb_34 <BR> FE NC gb_34 <BR> FE ND gb_34 </TT></P>
<P><TT>......... </TT><TT><BR> [ angles ] <BR>; ai aj ak gromos type <BR> -C N H ga_31 <BR> H N CA ga_17 <BR> -C N CA ga_30 <BR> N CA C ga_12 <BR> CA C +N ga_18 <BR> CA C O ga_29 <BR> ....... <BR> [ impropers ] <BR>; ai aj ak al gromos type<BR> N -C CA H gi_1 <BR> C CA +N O gi_1 <BR> CA N C CB gi_2 <BR> FE SG NA ND gi_3 <BR> FE SG NA NB gi_3 <BR> FE SG NB NC gi_3 <BR> FE SG NC ND gi_3 <BR> ......... <BR> [ dihedrals ] <BR>; ai aj ak al gromos type<BR> .........</TT><BR></P><SPAN title="neteasefooter">
<P>
</P><HR>
<P><A href="http://www.yeah.net/?from=footer">没有广告的终身免费邮箱,www.yeah.net</A> </P></SPAN><BR><BR><SPAN title="neteasefooter">
<P>
</P><HR>
<P><A href="http://www.yeah.net/?from=footer">没有广告的终身免费邮箱,www.yeah.net</A> </P></SPAN><br><br><span title="neteasefooter"/><hr/>
<a href="http://www.yeah.net/?from=footer">没有广告的终身免费邮箱,www.yeah.net</a>
</span>