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
