Re: [AMBER] pmemd.cuda error; Exiting due to the presence of inconsistent SHAKEH hydrogen clusters

From: David A Case <david.case.rutgers.edu>
Date: Sat, 21 Apr 2018 09:07:37 -0400

On Fri, Apr 20, 2018, Sadegh Faramarzi Ganjabad wrote:
>
> I know this error is related to the difference in naming of water molecules
> in CHARMM and AMBER, and it has been discussed before,
>
> But I can't find a solution for that. I am trying to run Amber inputs
> generated by Chamber, and to change the name of water molecules I added
> this line in the &cntrl section of my input
>
> WATNAM='TIP3',OWTNM='OH2', HWTNM1='H1',HWTNM2='H2',

Not sure this will work, but it's quite simple and worth a try:
Add spaces to make each name four characters long:

   WATNAM='TIP3',OWTNM='OH2 ', HWTNM1='H1 ',HWTNM2='H2 ',

If that fails, the parmed/chamber action in AmberTools18 should output Amber
standard names. (Again, I am guessing, but I think this is correct.)

Finally, you could just use a text editor to change the names in your
prmtop file manually.

(I haven't tested any of the above suggestions; but they seem worth
trying.)

...good luck....dac


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Received on Sat Apr 21 2018 - 06:30:04 PDT
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