<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV>Dear All,</DIV>
<DIV> </DIV>
<DIV>I am trying to use Charmm36 force field in Gromacs. I downloaded the ffcharm36 force field files created by Tom Piggot and Pär Bjelkmar from the user contribution in Gromacs website. Then I used the pdb2gmx to get the popc_c36.top using the following command:</DIV>
<DIV>pdb2gmx -f popc.pdb -o popc.gro -p popc_c36.top</DIV>
<DIV> </DIV>
<DIV>When I checked the popc topology file, I found that there are some dihedral terms missing in the topology file. For example, in the popc_c36.top file, atoms 3, 4, 5 are all methyl carbons, there should be three dihedral terms 3 1 2 17; 4 1 2 17 and 5 1 2 17.<BR>Unfortunately, there are only 3 1 2 17, the last two are missing, part of the popc_c36.top are shown below:</DIV>
<DIV>[ atoms ]<BR>; nr type resnr residue atom cgnr charge mass typeB chargeB massB<BR>; residue 1 POPC rtp POPC q 0.0<BR> 1 NTL 1 POPC N 1 -0.6 14.007 ; qtot -0.6<BR> 2 CTL2 1 POPC C12 2 -0.1 12.011 ; qtot -0.7<BR> 3
CTL5 1 POPC C13 3 -0.35 12.011 ; qtot -1.05<BR> 4 CTL5 1 POPC C14 4 -0.35 12.011 ; qtot -1.4<BR> 5 CTL5 1 POPC C15 5 -0.35 12.011 ; qtot -1.75<BR> 6 HL 1 POPC H12A 6
0.25 1.008 ; qtot -1.5<BR> 7 HL 1 POPC H12B 7 0.25 1.008 ; qtot -1.25<BR> 8 HL 1 POPC H13A 8 0.25 1.008 ; qtot -1<BR> 9 HL 1 POPC H13B 9 0.25 1.008 ; qtot -0.75<BR>
10 HL 1 POPC H13C 10 0.25 1.008 ; qtot -0.5<BR> 11 HL 1 POPC H14A 11 0.25 1.008 ; qtot -0.25<BR> 12 HL 1 POPC H14B 12 0.25 1.008 ; qtot 0<BR> 13 HL 1 POPC H14C
13 0.25 1.008 ; qtot 0.25<BR> 14 HL 1 POPC H15A 14 0.25 1.008 ; qtot 0.5<BR> 15 HL 1 POPC H15B 15 0.25 1.008 ; qtot 0.75<BR> 16 HL 1 POPC H15C 16 0.25 1.008 ; qtot 1<BR>
17 CTL2 1 POPC C11 17 -0.08 12.011 ; qtot 0.92<BR> 18 HAL2 1 POPC H11A 18 0.09 1.008 ; qtot 1.01<BR> 19 HAL2 1 POPC H11B 19 0.09 1.008 ; qtot 1.1<BR>.......</DIV>
<DIV>[ dihedrals ]<BR>; ai aj ak al funct c0 c1 c2 c3 c4 c5<BR> 3 1 2 17 1 <BR> 2 1 3 8 1 <BR> 2 1 4 11 1 <BR> 2 1
5 14 1 <BR> 1 2 17 23 1 <BR> 2 17 23 20 1 <BR> 21 20 23 17 1 <BR>........</DIV>
<DIV> </DIV>
<DIV>I also checked the dpc.itp in gromos force field from Tielman's website, which has been widely used by many people. There are also some missing dihedral terms in the dpc.itp file. </DIV>
<DIV>I am wondering if those missing dihedrals are neglected intentionally for gromos force field? When I use other force fields such as charmm/amber, do I need to add the missing dihedrals? If so, is there any way to do it instead of manually adding those missing dihedral terms?<BR><BR>Could anybody give some suggestions? Thanks very much!</DIV>
<DIV> </DIV>
<DIV>Cheers,</DIV>
<DIV>Jianguo</DIV><BR><BR></td></tr></table><br>