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

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 12 May 2010 15:20:13 -0400

Can you resend your email without the markup coding? I have a feeling many
people will not be able to understand your email.

On Wed, May 12, 2010 at 3:18 PM, Jayalakshmi Sridhar <jsridhar.xula.edu>wrote:

>
> <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. <br
> _moz_dirty="" />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 />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 <lt%3Bjsridhar.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<br
> />> 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<br
> />> tra jin ../2ns_md/2a6_md14.mdcrd > trajin ../2
> ns_md/2a6_md15.mdcrd > trajin ../10ns_md_h t/2a6_md18.mdcrd<br
> />> 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<br
> />> 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<br
> />> 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; -- <br
> />======== ======================== ========================
> =========== 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> =======================
> ======================== ==================== <
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-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed May 12 2010 - 12:30:07 PDT