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<DIV><FONT face=Arial color=#0000ff size=2><SPAN class=375162310-21062005>Hi
</SPAN></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=375162310-21062005> As you mentioned I had listed
the entries i made to all the parameter files ( ffoplsaa.atp ffoplsaa.rtp
ffoplsaanb.itp ffoplsaa.hdb ffoplsaabon.itp ) in my mail. i know the mail
was too long! </SPAN></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=375162310-21062005></SPAN></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=375162310-21062005>basically my question was -- </SPAN></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=375162310-21062005> is there
is any convention to be followed for naming hydrogens in any new molecule
? </SPAN></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=375162310-21062005></SPAN></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=375162310-21062005>-sandeep</SPAN></FONT></DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=375162310-21062005></SPAN></FONT> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2><SPAN
class=375162310-21062005></SPAN></FONT> </DIV>
<BLOCKQUOTE
style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #0000ff 2px solid; MARGIN-RIGHT: 0px">
<DIV></DIV>
<DIV class=OutlookMessageHeader lang=en-us dir=ltr align=left><FONT
face=Tahoma size=2>-----Original Message-----<BR><B>From:</B>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <B>On
Behalf Of </B>ÎâÏÔ»Ô<BR><B>Sent:</B> Tuesday, June 21, 2005 4:17
PM<BR><B>To:</B> Discussion list for GROMACS user<BR><B>Subject:</B> Re:
[gmx-users] OPLS, pdb2gmx and hydrogen nomenclature<BR><BR></FONT></DIV>
<DIV>You should create a new force field parameter for your molecule in the
ffoplsaa.rtp. In this file, you can create the parameters basing on the amino
acid residues. The bonded and non-bonded parameters can be got from the
ffoplsaa.itp and ffoplsaanb.itp..Good luck!</DIV>
<DIV> </DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV>
<HR>
</DIV>
<DIV>Hi</DIV>
<DIV> </DIV>
<DIV>I was trying to construct an OPLS topology for benzene by using PHE</DIV>
<DIV>residue parameters.</DIV>
<DIV> </DIV>
<DIV>I made local copies of ffopls* files and deleted everything except</DIV>
<DIV>entries related to my residue (listed at the end).</DIV>
<DIV> </DIV>
<DIV>My pdb files looks like (note first two lines):</DIV>
<DIV> </DIV>
<DIV>ATOM 1 CG BEN 1 42.710 25.370 54.530 1.00 0.000</DIV>
<DIV>ATOM 2 HG1 BEN 1 42.610 26.860 54.540 1.00 0.000</DIV>
<DIV>ATOM 3 CD1 BEN 1 43.930 24.740 54.620 1.00 0.000</DIV>
<DIV>ATOM 4 HD1 BEN 1 44.770 25.280 54.700 1.00 0.000</DIV>
<DIV>ATOM 5 CD2 BEN 1 41.570 24.590 54.430 1.00 0.000</DIV>
<DIV>ATOM 6 HD2 BEN 1 40.670 25.040 54.380 1.00 0.000</DIV>
<DIV>ATOM 7 CE1 BEN 1 44.030 23.350 54.600 1.00 0.000</DIV>
<DIV>ATOM 8 HE1 BEN 1 44.930 22.910 54.670 1.00 0.000</DIV>
<DIV>ATOM 9 CE2 BEN 1 41.650 23.210 54.400 1.00 0.000</DIV>
<DIV>ATOM 10 HE2 BEN 1 40.810 22.670 54.330 1.00 0.000</DIV>
<DIV>ATOM 11 CZ BEN 1 42.880 22.590 54.480 1.00 0.000</DIV>
<DIV>ATOM 12 HZ BEN 1 42.940 21.590 54.460 1.00 0.000</DIV>
<DIV> </DIV>
<DIV>Now</DIV>
<DIV> pdb2gmx -f mypdb.pdb -missing</DIV>
<DIV>results in topol.top:</DIV>
<DIV>[ atoms ]</DIV>
<DIV>; nr type resnr residue atom cgnr charge mass</DIV>
<DIV>typeB</DIV>
<DIV> 1 opls_145 1 BEN CG 1 -0.115 12.011</DIV>
<DIV> 2 opls_146 1 BEN HG 1 0.115 1.008</DIV>
<DIV> 3 opls_146 1 BEN HG1 1 0.115 1.008</DIV>
<DIV>...</DIV>
<DIV> </DIV>
<DIV>My question is:</DIV>
<DIV>Where has atom HG come from ?! it is not in any of the parameter files.</DIV>
<DIV> </DIV>
<DIV>but with the -ignh flag HG1 is removed while HG is generated.</DIV>
<DIV> </DIV>
<DIV>does pdb2gmx have a constraint on the nomenclature of hydrogens ?</DIV>
<DIV> </DIV>
<DIV>Thnx in advance ..</DIV>
<DIV>sandeep</DIV>
<DIV> </DIV>
<DIV>*************************************************</DIV>
<DIV>Parameter file listing -</DIV>
<DIV><FONT face=Arial color=#0000ff size=2></FONT> </DIV>
<DIV>ffoplsaa.atp</DIV>
<DIV>------------</DIV>
<DIV> </DIV>
<DIV> opls_145 12.01100 ;</DIV>
<DIV> opls_146 1.00800 ; Benzene H - 12 site.</DIV>
<DIV> </DIV>
<DIV>ffoplsaa.rtp</DIV>
<DIV>------------</DIV>
<DIV>[ BEN ]</DIV>
<DIV> [ atoms ]</DIV>
<DIV> CG opls_145 -0.115 2</DIV>
<DIV> HG1 opls_146 0.115 2 ; <
</DIV>
<DIV>-- NOTE: HG1, not HG</DIV>
<DIV> CD1 opls_145 -0.115 3</DIV>
<DIV> HD1 opls_146 0.115 3</DIV>
<DIV> CD2 opls_145 -0.115 4</DIV>
<DIV> HD2 opls_146 0.115 4</DIV>
<DIV> CE1 opls_145 -0.115 5</DIV>
<DIV> HE1 opls_146 0.115 5</DIV>
<DIV> CE2 opls_145 -0.115 6</DIV>
<DIV> HE2 opls_146 0.115 6</DIV>
<DIV> CZ opls_145 -0.115 7</DIV>
<DIV> HZ opls_146 0.115 7</DIV>
<DIV> [ bonds ]</DIV>
<DIV> CG HG1</DIV>
<DIV> CG CD1</DIV>
<DIV> CG CD2</DIV>
<DIV> CD1 HD1</DIV>
<DIV> CD1 CE1</DIV>
<DIV> CD2 HD2</DIV>
<DIV> CD2 CE2</DIV>
<DIV> CE1 HE1</DIV>
<DIV> CE1 CZ</DIV>
<DIV> CE2 HE2</DIV>
<DIV> CE2 CZ</DIV>
<DIV> CZ HZ</DIV>
<DIV> [ impropers ]</DIV>
<DIV> CG CE2 CD2 HD2 improper_Z_CA_X_Y</DIV>
<DIV> CD2 CZ CE2 HE2 improper_Z_CA_X_Y</DIV>
<DIV> CE1 CE2 CZ HZ improper_Z_CA_X_Y</DIV>
<DIV> CD1 CZ CE1 HE1 improper_Z_CA_X_Y</DIV>
<DIV> CG CE1 CD1 HD1 improper_Z_CA_X_Y</DIV>
<DIV> CD1 CD2 CG HG1 improper_Z_CA_X_Y</DIV>
<DIV> </DIV>
<DIV>ffoplsaanb.itp</DIV>
<DIV>--------------</DIV>
<DIV>[ atomtypes ]</DIV>
<DIV>; name bond_type mass charge ptype sigma epsilon</DIV>
<DIV> opls_145 CA 12.01100 -0.115 A 3.55000e-01</DIV>
<DIV>2.92880e-01</DIV>
<DIV>opls_146 HA 1.00800 0.115 A 2.42000e-01 1.25520e-01</DIV>
<DIV> </DIV>
<DIV>ffoplsaa.hdb</DIV>
<DIV>------------</DIV>
<DIV>BEN 6</DIV>
<DIV>1 1 CG CD1 CD2</DIV>
<DIV>1 1 CD1 CG CE1</DIV>
<DIV>1 1 CD2 CG CE2</DIV>
<DIV>1 1 CE1 CD1 CZ</DIV>
<DIV>1 1 CE2 CD2 CZ</DIV>
<DIV>1 1 CZ CE1 CE2</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>ffoplsaabon.itp</DIV>
<DIV>---------------</DIV>
<DIV>[ bondtypes ]</DIV>
<DIV>; i j func b0 kb</DIV>
<DIV> CA CA 1 0.14000 392459.2 ; TRP,TYR,PHE</DIV>
<DIV> CA HA 1 0.10800 307105.6 ; PHE, etc.</DIV>
<DIV> </DIV>
<DIV>[ angletypes ]</DIV>
<DIV>; i j k func th0 cth</DIV>
<DIV> CA CA CA 1 120.000 527.184 ; PHE(OL)</DIV>
<DIV> CA CA HA 1 120.000 292.880 ;</DIV>
<DIV> </DIV>
<DIV>[ dihedraltypes ]</DIV>
<DIV>; i j k l func coefficients</DIV>
<DIV> X CA CA X 3 30.33400 0.00000 -30.33400</DIV>
<DIV>0.00000 0.00000 0.00000 ; aromatic ring</DIV>
<DIV> </DIV>
<DIV>[ dihedraltypes ]</DIV>
<DIV>; Z -CA-X -Y improper torsion. CA is any ring carbon</DIV>
<DIV>(CA,CB,CN,CV,CW,CR,CK,CQ,CS,C*)</DIV>
<DIV>#define improper_Z_CA_X_Y 180.0 4.60240 2</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV>_______________________________________________</DIV>
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