[AMBER] Edit prmtop file

From: Paul Mortenson <P.Mortenson.astex-therapeutics.com>
Date: Wed, 13 Jul 2011 09:37:53 +0100

Dear AMBER users,

I have a prmtop file corresponding to an explicitly solvated protein,
and I would like to create a second prmtop file that is near identical,
but has exactly one fewer water molecules. I have been using the rdparm
program to do this, via the "stripwater" command, and it works fine when
the solvent is TIP3P, but not TIP4P - rdparm fails to recognise the
presence of any waters in this case. I have tested this for rdparm from
AMBER9, and also from AmberTools 1.5.

I have looked through the AmberTools manual, and cpptraj claims to be
able to write modified prmtop files, but with the caveat that they are
only suitable for visualisation, not simulation. I need to be able to
pass my modified prmtop file to sander.

Is there a way of doing this without having to write some code to modify
the prmtop file myself?

Thanks,
Paul




Disclaimer
This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing P.Mortenson.astex-therapeutics.com and destroy all copies of the message and any attached documents.
Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof.
Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 13 2011 - 02:00:02 PDT
Custom Search