<DIV><includetail>
<DIV>Dear gmxers,</DIV>
<DIV> I have reinstalled the gmx-4.5.1 and this time the pdb2gmx is found to work using the same input and parameter files. So I consider that the "very strange" problem is due to some modified file which is unknown yet for me. Thanks again for your attention.</DIV>
<DIV>Sincerely, yours</DIV>
<DIV>Chaofu Wu, Dr.</DIV>
<DIV style="COLOR: #000">
<DIV style="PADDING-RIGHT: 0px; PADDING-LEFT: 0px; FONT-SIZE: 12px; PADDING-BOTTOM: 2px; PADDING-TOP: 2px; FONT-FAMILY: Arial Narrow">------------------ 原始邮件 ------------------</DIV>
<DIV style="PADDING-RIGHT: 8px; PADDING-LEFT: 8px; FONT-SIZE: 12px; BACKGROUND: #efefef; PADDING-BOTTOM: 8px; PADDING-TOP: 8px">
<DIV id=menu_sender><B>发件人:</B> "Justin A. Lemkul"<jalemkul@vt.edu>;</DIV>
<DIV><B>发送时间:</B> 2010年10月17日(星期天) 晚上8:21</DIV>
<DIV><B>收件人:</B> "Discussion list for GROMACS users"<gmx-users@gromacs.org>; <WBR></DIV>
<DIV></DIV>
<DIV><B>主题:</B> Re: [gmx-users] A very strange problem about version of pdb2gmx</DIV><BR>英雄不再寂寞 wrote:<BR>> Dear gmxers,<BR>> Yesterday, I posted a mail titled "pdb2gmx stop at "AtomType 1" " <BR>> where I mentioned that I used gmx-4.5.1. The resulting problem is again <BR>> posted below. Today, I turn to the gmx-4.0.7, and use the same pdb <BR>> and rtp files with the name modified to compatible to the version. <BR>> Strangely, it is found that the pdb2gmx of this version can generate the <BR>> top file without any errors. Could you give me clues to why the latest <BR>> version can not whereas the older version can? To get the clear help, my <BR>> pdb and rtp files are also posted below. Thanks a lot for any reply.<BR><BR>Your system works for me under version 4.5.1, after fixing the naming mismatch <BR>you have between your .pdb file ("MOL") and .rtp file ("DET"). I suppose your <BR>actual input files have the correct names, though, otherwise this combination <BR>would have generated a fatal error, not a hang.<BR><BR>-Justin<BR><BR>> Chaofu Wu, Dr.<BR>> <BR>> My command line and the screen output:<BR>> xiaowu759@linux-s38y:~/workshop <BR>> <mailto:xiaowu759@linux-s38y:~/workshop>> pdb2gmx -f deta.pdb -o <BR>> deta.gro -p deta.top -i deta.itp -ter<BR>> :-) G R O M A C S (-:<BR>> Gromacs Runs One Microsecond At Cannonball Speeds<BR>> :-) VERSION 4.5.1 (-:<BR>> ......<BR>> Opening force field file oplsaa.ff/aminoacids.r2b<BR>> Reading deta.pdb...<BR>> Read 20 atoms<BR>> Analyzing pdb file<BR>> Splitting PDB chains based on TER records or changing chain id.<BR>> There are 1 chains and 0 blocks of water and 1 residues with 20 atoms<BR>> chain #res #atoms<BR>> 1 ' ' 1 20 <BR>> All occupancies are one<BR>> Opening force field file oplsaa.ff/atomtypes.atp<BR>> Atomtype 1<BR>> <BR>> My pdb file:<BR>> ATOM 1 N1 MOL 1 -5.199 1.343 0.334 1.00 <BR>> 0.00 N <BR>> ATOM 2 C2 MOL 1 -4.582 0.639 1.470 1.00 <BR>> 0.00 C <BR>> ATOM 3 C3 MOL 1 -3.897 1.462 2.593 1.00 <BR>> 0.00 C <BR>> ATOM 4 N4 MOL 1 -3.194 0.615 3.574 1.00 <BR>> 0.00 N <BR>> ATOM 5 C5 MOL 1 -2.373 1.331 4.566 1.00 <BR>> 0.00 C <BR>> ATOM 6 C6 MOL 1 -1.520 0.397 5.464 1.00 <BR>> 0.00 C <BR>> ATOM 7 N7 MOL 1 -0.684 1.133 6.432 1.00 <BR>> 0.00 N <BR>> ATOM 8 H12 MOL 1 -4.614 2.067 -0.035 1.00 <BR>> 0.00 H <BR>> ATOM 9 H11 MOL 1 -6.128 1.694 0.483 1.00 <BR>> 0.00 H <BR>> ATOM 10 H22 MOL 1 -3.826 -0.053 1.056 1.00 <BR>> 0.00 H <BR>> ATOM 11 H21 MOL 1 -5.345 -0.016 1.926 1.00 <BR>> 0.00 H <BR>> ATOM 12 H31 MOL 1 -4.628 2.144 3.065 1.00 <BR>> 0.00 H <BR>> ATOM 13 H32 MOL 1 -3.141 2.116 2.124 1.00 <BR>> 0.00 H <BR>> ATOM 14 H41 MOL 1 -3.854 0.018 4.043 1.00 <BR>> 0.00 H <BR>> ATOM 15 H51 MOL 1 -2.980 2.003 5.204 1.00 <BR>> 0.00 H <BR>> ATOM 16 H52 MOL 1 -1.679 1.992 4.016 1.00 <BR>> 0.00 H <BR>> ATOM 17 H62 MOL 1 -0.857 -0.180 4.795 1.00 <BR>> 0.00 H <BR>> ATOM 18 H61 MOL 1 -2.188 -0.346 5.939 1.00 <BR>> 0.00 H <BR>> ATOM 19 H72 MOL 1 -0.023 0.541 6.916 1.00 <BR>> 0.00 H <BR>> ATOM 20 H71 MOL 1 -1.253 1.554 7.143 1.00 <BR>> 0.00 H <BR>> TER<BR>> My rtp file:<BR>> [ DET ]<BR>> [ atoms ]<BR>> N1 opls_900 -0.900 1<BR>> H11 opls_909 0.360 1<BR>> H12 opls_909 0.360 1<BR>> C2 opls_906 0.060 1<BR>> H21 opls_911 0.060 1<BR>> H22 opls_911 0.060 1<BR>> C3 opls_907 0.080 2<BR>> H31 opls_911 0.060 2<BR>> H32 opls_911 0.060 2<BR>> N4 opls_901 -0.780 2<BR>> H41 opls_910 0.380 2<BR>> C5 opls_907 0.080 2<BR>> H51 opls_911 0.060 2<BR>> H52 opls_911 0.060 2<BR>> C6 opls_906 0.060 3<BR>> H61 opls_911 0.060 3<BR>> H62 opls_911 0.060 3<BR>> N7 opls_900 -0.900 3<BR>> H71 opls_909 0.360 3<BR>> H72 opls_909 0.360 3<BR>> [ bonds ]<BR>> N1 H11<BR>> N1 H12<BR>> N1 C2<BR>> C2 H21<BR>> C2 H22<BR>> C2 C3<BR>> C3 H31<BR>> C3 H32<BR>> C3 N4<BR>> N4 H41<BR>> N4 C5<BR>> C5 H51<BR>> C5 H52<BR>> C5 C6<BR>> C6 H61<BR>> C6 H62<BR>> C6 N7<BR>> N7 H71<BR>> N7 H72<BR>> <BR>> <BR><BR>-- <BR>========================================<BR><BR>Justin A. Lemkul<BR>Ph.D. Candidate<BR>ICTAS Doctoral Scholar<BR>MILES-IGERT Trainee<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></includetail></DIV>