Hi,
Thanks for the pointers. I figured it out. It is because of the two missing residues in the front of my reference. The reference resid starts from 3 instead of 1. But I guess in the rmsd selection, no matter how residues are number in the pdb, the internal resid (starting from 1) is always used. So if I change the rms line to
rms reference :3.CA :1.CA nofit out rmsd_test2.plo
The resulting rmsd values match.
Thanks a lot! Glad it's resolved.
Thanks,
Huan
-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Friday, February 09, 2018 4:36 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] RMSD with cpptraj
Hi,
As Carlos said, you have to ensure that you have the same atom ordering between your reference and target structures. As a test, make sure you get an RMSD that makes sense when you use the first frame as your reference. You mentioned that the reference was two residues short, so you need to choose a sensible mask for the reference that matches the target.
-Dan
On Fri, Feb 9, 2018 at 4:29 PM, Rui, Huan <hrui.amgen.com> wrote:
> Here's some follow up. Even if all the heavy atoms have the same order, the larger computed RMSD problem persists. I'm not really sure what is wrong here.
>
> -----Original Message-----
> From: Rui, Huan
> Sent: Friday, February 09, 2018 2:51 PM
> To: 'AMBER Mailing List' <amber.ambermd.org>
> Subject: RE: [AMBER] RMSD with cpptraj
>
> A correction. The CA and backbone atoms do have the same order but not the sidechain heavy atoms.
>
> -----Original Message-----
> From: Rui, Huan
> Sent: Friday, February 09, 2018 2:46 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: RE: [AMBER] RMSD with cpptraj
>
> Thanks for the reply, Carlos. The heavy atoms do have the same order but the reference structure does not have hydrogens. The reference structure is also 2 residues shorter even though the missing residues are not included in the RMS calculation command. Could any of the two be the issue?
>
> -----Original Message-----
> From: Carlos Simmerling [mailto:carlos.simmerling.gmail.com]
> Sent: Friday, February 09, 2018 2:41 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] RMSD with cpptraj
>
> are the atoms in the same order in the pdb file as in the trajectory file?
>
> On Fri, Feb 9, 2018 at 2:38 PM, Rui, Huan <hrui.amgen.com> wrote:
>
>> Hi all,
>>
>>
>>
>> I'm trying to use cpptraj to compute the RMSD between my trajectory
>> and a crystal structure. The script works fine, but the RMSD values
>> seems incorrect. My reference is this clean_update.pdb. it has the
>> same residues as the protein in my trajectory. The first rms command
>> produced RMSD at around 6 Ang for all the snapshots, but when I look
>> at the final structure overlay produced by my "trajout" command, the
>> two structures do not look like they are 6 Ang apart. Also after the
>> alignment from the first rms command, I wrote down the distance
>> between two CA atoms from resid 100, the output rmsd_test2.plo show
>> that they are 4 Ang apart, though in the superposed pdb files they
>> are only 0.5 Ang away. Here's how my cpptraj script look like:
>>
>>
>>
>> trajin step4_1.nc 1 500 1
>>
>> parm clean_update.pdb
>>
>> reference clean_update.pdb parm clean_update.pdb
>>
>> autoimage :1-170
>>
>> rms reference :3-165.CA :3-165.CA out rmsd_test.plo
>>
>> rms reference :100.CA :100.CA nofit out rmsd_test2.plo
>>
>> trajout testrmsd.pdb onlyframes 500
>>
>> run
>>
>> quit
>>
>>
>>
>> Could anybody give me some insights on why this is?
>>
>>
>>
>> Thank you very much in advance.
>>
>>
>>
>> Thanks,
>>
>> Huan
>>
>>
>>
>>
>>
>>
>>
>>
>>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
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Received on Fri Feb 09 2018 - 14:00:04 PST
