Unable to eliminate overall Translational and rotational Motion

Mandira Dinda

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Oct 11, 2023, 11:58:32 AM10/11/23

to carma molecular dynamics

Hello,

My system is 1500 ns simulated Trajectory not having any ligand bound.I want to calculate Entropy (Schlitter) of the system. When I try to eliminate the overall translational and rotational using the command :

carma -v -fit -atmid ALLID -segid A my.dcd protein.psf

Less than two " " atoms found for segid "A ". Abort.

I had generate my dcd and psf file using VMD from xtc file and pdb file respectively for the protein only.

please suggest something why this is happen

Thank You,

Regards

Mandira Dinda

Nicholas M. Glykos

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Oct 11, 2023, 12:08:13 PM10/11/23

to Mandira Dinda, carma molecular dynamics

> Less than two " " atoms found for segid "A ". Abort.

Examine the PSF file, and find -and then use- the correct SEGID of your protein.
For example, in this file :

PSF

1 !NTITLE
REMARKS VMD-generated NAMD/X-Plor PSF structure file

7400 !NATOM
1 A 1 VAL N N3 0.057700 14.0100 0
2 A 1 VAL H1 H 0.227200 1.0080 0
3 A 1 VAL H2 H 0.227200 1.0080 0
4 A 1 VAL H3 H 0.227200 1.0080 0
5 A 1 VAL CA CT -0.005400 12.0100 0
6 A 1 VAL HA HP 0.109300 1.0080 0
7 A 1 VAL CB CT 0.319600 12.0100 0
...............
...............

the SEGID is "A". In your case it will be something different.

--

Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, https://utopia.duth.gr/glykos/

Mandira Dinda

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Oct 12, 2023, 1:29:27 AM10/12/23

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Hello,

Thank you for your prompt reply.I had already corrected the SEGID as "A" in PSF file after generating it through VMD before using it.I have also tried using the PSF file generated by CHARMM-GUI.But it is aborted in same manner.

Thank you,

Regards

Mandira Dinda

Nicholas M. Glykos

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Oct 12, 2023, 3:20:19 AM10/12/23

to Mandira Dinda, carma molecular dynamics

> Thank you for your prompt reply.I had already corrected the SEGID as "A" in
> PSF file after generating it through VMD before using it.I have also tried
> using the PSF file generated by CHARMM-GUI.But it is aborted in same
> manner.

We can not make progress trying to guess what is wrong. Send the output of

head -100 protein.psf

Mandira Dinda

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Oct 12, 2023, 5:28:01 AM10/12/23

to carma molecular dynamics

I have successfully calculated the entropy of my system using PSF file generated by CHARMM-GUI by correcting the SEGID as "A".

Thank you

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