Re: [AMBER] Ptraj image problems from Jayalakshmi Sridhar on 2010-05-12 (Amber Archive May 2010)

From: Jayalakshmi Sridhar <jsridhar.xula.edu>
Date: Wed, 12 May 2010 14:18:35 -0500

<div style="font-family: 'Times New Roman'; font-size: 1 6px;">I generated the prmtop file with xleap. I had initially ge nerated two prmtop files- one with periodic box with water and another w ithout the periodic box and water. I used the prmtop without box and w ater for imaging in vmd. I do not see any of the solvent water molecul es. I only see the protein atoms streaking in a cube shaped box. One other discrepancy that I see it that it should have 2400 frames (earlie= r
 .binpos loading), but the image ptraj output shows 11887 frames. Jaya. O= n
 05/12/10, Carlos Simmerling &lt ;carlos.simmerling.gmail.com>wrote:<block quotecite="mid:AANLkTimuVOj2U-bFWUTkvrsBEimLPBxxEQWJLH9KmQNT.ma il.gmail.com" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt; " type="cite"><div class="mimepart text plain">vmd c an't load the traj file directly, so you need to tell us how you<b= r
 />generated the prmtop or pdb that you used in vmd prior to loadingt he traj file. it should be exactly what you made in ptraj- sa= me
 system but no water and no periodic box. On 5/12/10, Jayalakshmi Sridhar <jsridhar.xula.edu&g t; wrote: > Dear Amber Users, > I have run MD on my protein for 12ns. I was able to combine all the MD > trajectories into one .binpos file. When I try to im age the protein using > ptraj, I run into problems. The output .mdcrd does not load well in VMD. The > a toms seem to be streaking all over the box. The ptraj script I used is > given below: ANy help to resolve this problem is gr eatly appreciated. > Thanks. > Jaya. > > trajin ../2ns_md/2a6_md2. mdcrd 1 500 25 > trajin ../2ns_md/2a6_md3.mdcr= d
 1 500 25 > trajin ../2ns_md/2a6_md4.mdcrd 1 = 500
 25 > trajin ../2ns_md/2a6_md5.mdcrd 1 500 25 > trajin ../2ns_md/2a6_md6.mdcrd 1 500 25 > trajin ../2ns_md/2a6_md7.mdcrd > trajin ../2ns_md/2a6_md8.mdcrd > trajin .. /2ns_md/2a6_md9.mdcrd > trajin ../2ns_md/2a6 _md10.mdcrd > trajin ../2ns_md/2a6_md11.md crd > trajin ../2ns_md/2a6_md12.mdcrd > trajin ../2ns_md/2a6_md13.mdcrd > tra jin ../2ns_md/2a6_md14.mdcrd > trajin ../2 ns_md/2a6_md15.mdcrd > trajin ../10ns_md_h t/2a6_md18.mdcrd > trajin ../10ns_md_ht/2a6_ md19.mdcrd > trajin ../10ns_md_ht/2a6_md20. mdcrd > trajin ../10ns_md_ht/2a6_md21.mdcrd > trajin ../10ns_md_ht/2a6_md22.mdcrd > trajin ../10ns_md_ht/2a6_md23.mdcrd > trajin ../10ns_md_ht/2a6_md24.mdcrd > traji= n
 ../10ns_md_ht/2a6_md25.mdcrd > trajin .. /10ns_md_ht/2a6_md26.mdcrd > trajin ../10ns_ md_ht/2a6_md27.mdcrd > trajin ../10ns_md_h t/2a6_md28.mdcrd > trajin ../10ns_md_ht/2a6_ md29.mdcrd > trajin ../10ns_md_ht/2a6_md30. mdcrd > trajin ../10ns_md_ht/2a6_md31.mdcrd > trajin ../10ns_md_ht/2a6_md32.mdcrd > trajin ../10ns_md_ht/2a6_md33.mdcrd > trajout 2a6_md_2_33.mdcrd nobox > center :1-4= 65
 mass origin > image origin center > r= ms
 first mass out rms_to_first.data :1-465 > ave= rage
 avg.pdb :1-465 pdb > strip :WAT &g= t;
 go > > > & gt; -- ======== ======================== ======================== =========== Carlos L. Simmerling, Ph. D. Professor, Department of Chemistry CMM Bldg, Room G80 Phone: (631) 632-1336 Fax : 632-1555 Stony Brook University E-mail: carlos.simmerling.gmail.com Stony Brook, NY 11794-5115 Web: <a href="http://www.simmerlinglab.org" t arget="_blank">http://www.simmerlinglab.org</a> ======================= ======================== ==================== ______________________ ________________________ _ AMBER mailing list AMBER.ambermd.org <a href="http://lists.ambermd.org/mailman/listinfo/amber" target="_blank">http://lists.ambermd.org/mailman/listinf o/amber</a> </div></blockquote></div>

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Received on Wed May 12 2010 - 12:30:06 PDT