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Hi<br>I don't have a .tpr file for the cg system. I am anlayzing results from pca and the trajectories only have calpha atoms.<br>Can I generate a .tpr for just calpha?
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<div dir="ltr"><br><br><div><div id="SkyDrivePlaceholder"></div>> Date: Sun, 27 May 2012 12:12:14 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] trjconv -conect<br>> <br>> <br>> <br>> On 5/27/12 12:05 PM, vijaya subramanian wrote:<br>> ><br>> > Hi<br>> > I am trying to add conect records to a cg trajectory under gromacs 4.5.4 as follows:<br>> > trjconv -s CONECT.PDB -f traj.xtc -conect -o testconect.pdb<br>> ><br>> > or with one frame<br>> ><br>> > trjconv -s CONECT.PDB -f oneframe.pdb -conect -o testconect.pdb<br>> ><br>> > but dont see any conect records in the output file.<br>> ><br>> > The conect records are in the input to -s , conect.pdb and in the following format:<br>> > ...<br>> > ATOM 4125 CA HIS X 173 107.816 143.564 71.946 1.00 0<br>> > ATOM 4126 CA THR X 174 110.288 142.372 69.327 1.00 0<br>> > ATOM 4127 CA LEU X 175 111.958 139.227 70.607 1.00 0<br>> > ATOM 4128 CA GLY X 176 108.771 138.107 72.357 1.00 0<br>> > CONECT 1 2<br>> > CONECT 2 3<br>> > CONECT 3 4<br>> > CONECT 4 5<br>> > CONECT 5 6<br>> > CONECT 6 7<br>> > CONECT 7 8<br>> > CONECT 8 9<br>> > CONECT 9 10<br>> > CONECT 10 11<br>> > CONECT 11 12<br>> > CONECT 12 13<br>> > CONECT 13 14<br>> > CONECT 14 15<br>> > CONECT 15 16<br>> > CONECT 16 17<br>> > CONECT 17 18<br>> > CONECT 18 19<br>> > CONECT 19 20<br>> > CONECT 20 21<br>> > CONECT 21 22<br>> > ...<br>> ><br>> > What should I do differently to get the conect records in the output file?<br>> ><br>> ><br>> <br>> Try using a .tpr file, where bonds are present according to the topology.<br>> <br>> -Justin<br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul, Ph.D.<br>> Research Scientist<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br></div></div>
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