I listened to you absolutely and didn't proceed any other way! What I created in .rtp file for FVAL ( like what you described sometime ago), is as below: First of all added the FVAL to residuetyes.dat.
Then added to .rtp file: [ FVAL ] [ atoms ] CN C 0.357 0 ON O -0.51 1 H1 HA 0.100 2 N NH1 -0.423 3 HN H 0.333 4 CA CT1 0.034 5 HA HB 0.09 6 CB CT1 -0.093 7 HB HA 0.09 8 CG1 CT3 -0.268 9 HG11 HA 0.09 10 HG12 HA 0.09 11 HG13 HA 0.09 12 CG2 CT3 -0.268 13 HG21 HA 0.09 14 HG22 HA 0.09 15 HG23 HA 0.09 16 C C 0.528 17 O O -0.510 18 [ bonds ] CN H1 CN ON CN N N H CA N CA HA CA C C O CA CB CB HB CB CG1 CB CG2 CG2 HG21 CG2 HG22 CG2 HG23 CG1 HG11 CG1 HG12 CG1 HG13 [ impropers ] CN N ON H1 And at last adding H atoms to .hdb: 1 1 H1 C N O 1 1 HN N C CA 1 5 HA CA N C CB 1 5 HB CB CA CG1 CG2 3 4 HG1 CG1 CB CA 3 4 HG2 CG2 CB CA I tried to follow your suggestion exactly! Believe me! :-) Sincerely, Shima ________________________________ From: Justin Lemkul <jalem...@vt.edu> To: Shima Arasteh <shima_arasteh2...@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Sunday, July 29, 2012 1:14 AM Subject: Re: [gmx-users] Diagnosing + system blowing up On 7/28/12 2:47 PM, Shima Arasteh wrote: > > > > Dear Mark, Thanks for your suggestions. > Atom 1 is the C which is expected to connect to the H ( atom 18) . Atom 5 is > tha CA of the next resisue ( Valine), the bond 18-5 is not expected at all! > However I see this pair in the [pairs] section of topology ! > So I can get the result of an inappropriate bond interaction here! Correct? > Now I think it's not necessary to go through the diagnosing steps any more! > :-( > What is my duty right now?! > > Is this problem supposed to be fixed in the .pdb file? What's wrong with the > pdb file? What about erasing the unexpected bond interactions in topology > file? > You'll need to back up and provide more information here. I recall our discussion several weeks ago about this formylated valine problem, which was solved by creating a special residue called FVAL. If you created a correct .rtp entry like I described, this shouldn't be happening. If you're proceeded some other way, you will have to specify exactly what you've done up to this point. This may require snippets of relevant residues in coordinate files, .rtp entries, etc. Without this information, everything I've seen thus far is a jumbled mess that is nearly impossible for anyone on this list to troubleshoot. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
