it might be fine, but this suggests you might also want to check the
solvent pointers in the prmtop and make sure HOH is considered solvent
as well as the WAT.
On Fri, Apr 8, 2011 at 2:59 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Marc,
>
> This problem is due to you having solvent molecules with different names in
> the prmtop file. I came across it myself recently and have it on the list of
> things to fix. Essentially you likely have water in your prmtop called both
> HOH (from crystal structure) and WAT (from solvatebox). Leap should really
> take care of this and make the naming consistent but it doesn't.
>
> The best approach is probably to go back to your pdb file and rename all the
> crystal waters WAT and then build the prmtop again. Alternatively you can
> replace all occurances of HOH in the prmtop with WAT and 'I think' this
> should then work fine.
>
> If this is not the problem, or a subtly different occurrence of it please
> let me know the details of how you built your prmtop and I can look into it
> some more.
>
> All the best
> Ross
>
>> -----Original Message-----
>> From: Marc van der Kamp [mailto:marcvanderkamp.gmail.com]
>> Sent: Friday, April 08, 2011 8:07 AM
>> To: amber.ambermd.org
>> Subject: [AMBER] pmemd.cuda crashes due to "Inconsistent hydrogen
>> network"
>>
>> Hi all,
>>
>> I have previously successfully run pmemd.cuda_SPDP using an AMBER force
>> field.
>> I'm now trying to do the same using the CHARMM force field. After
>> converting
>> psf/crd using CHAMBER to prmtop/inpcrd, sander.MPI and pmemd.MPI have
>> no
>> problems with my system/files. However, when I try to run the same on a
>> GPU,
>> pmemd.cuda_SPDP crashes with the following message:
>> Inconsistent hydrogen network, exiting.
>>
>> I noticed this error message was introduced (or altered) in the
>> comprehensive Bugfix.9 (BTW, all current bugfixes, i.e. up to 12, are
>> applied):
>>
>> if ((my_nonfastwat_bond_dat[j].atm_i == atm_j) ||
>> (my_nonfastwat_bond_dat[j].atm_i == atm_j))
>>
>> {
>>
>> printf("Inconsistent hydrogen network,
>> exiting.\n");
>>
>> + gpu_shutdown_();
>>
>> exit(-1);
>>
>> }
>>
>> The error occurs right after the number of triangulated waters are
>> reported
>> in the output ("Number of triangulated 3-point waters found")
>>
>> FYI, I'm running on an NVIDIA Tesla M2050.
>>
>> Any suggestions on how to fix this?
>>
>> Many thanks in advance,
>> Marc
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
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>
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Received on Fri Apr 08 2011 - 12:30:06 PDT
