Oops.
In that case you can try this,
Import your prmtop and mdcrd file in vmd
And save the last frame as rst or crd file. Remember to export all atoms (including waters, ions etc)
Once you are done, check if the number of atoms in prmtop and newly exported rst/crd file is same.
Also check the box information.
Hope this works
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12
-----Original Message-----
From: Lovika Mittal [mailto:lovika.mittal.thsti.res.in]
Sent: Tuesday, March 07, 2017 10:29 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Query regarding extension of Molecular dynamics simulation from 50ns to 100ns
I did not give the option of creating md.rst file while running md, but i have .mdcrd file for 50ns . So, is it possible to extend MD simulation with .mdcrd file.
On Tue, Mar 7, 2017 at 10:05 AM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> Hello,
> If you were able to complete upto 50 ns, then what happened to the rst
> file??
>
>
> Best Regards
>
>
>
> Elvis Martis
> Ph.D. Student (Computational Chemistry) at Bombay College of Pharmacy
>
>
> A Kalina, Santacruz [E], Mumbai 400098, INDIA
> W www.elvismartis.in
> Skype. adrian_elvis12
>
>
>
>
> -----Original Message-----
> From: Lovika Mittal [mailto:lovika.mittal.thsti.res.in]
> Sent: Tuesday, March 07, 2017 9:56 AM
> To: amber.ambermd.org
> Subject: [AMBER] Query regarding extension of Molecular dynamics
> simulation from 50ns to 100ns
>
> Dear Sir/Madam,
> I would like to know how to extend the MD simulation of a protein-ligand
> complex from 50ns to 100 ns if we do not have md.rst file.
> I look forward to hearing from you soon.
>
> Thanking You.
>
> --
> *Lovika Mittal*
> *Junior Research Fellow*
> *D*rug *D*iscovery *R*esearch *C*entre *(DDRC)* *T*ranslational *H*ealth
> *S*cience and *T*echnology *I*nstitute (*THSTI*), NCR Biotech Science
> Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad-121001,
> Haryana, India.
> Mail- lovika93.gmail.com, lovika.mittal.thsti.res.in
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Lovika Mittal*
*Junior Research Fellow*
*D*rug *D*iscovery *R*esearch *C*entre *(DDRC)*
*T*ranslational *H*ealth *S*cience and *T*echnology *I*nstitute (*THSTI*),
NCR Biotech Science Cluster,
3rd Milestone, Faridabad-Gurgaon Expressway,
Faridabad-121001, Haryana, India.
Mail- lovika93.gmail.com, lovika.mittal.thsti.res.in
_______________________________________________
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Received on Mon Mar 06 2017 - 21:30:02 PST
