From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Fri May 26 2017 - 17:09:53 CDT
You wouldn't happen to be running a memory-optimized version of NAMD,
would you? The only documentation I can find suggests this shouldn't be
needed, since alchemify was incorparated into NAMD itself, except for
*possibly* memopt versions, which are typically only required for
running massive multimillion atom simulations.
On 05/26/2017 04:04 PM, Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES
SPACE RESEARCH ASSOCIATION] wrote:
> Hi Josh,
> Thanks for your response. It seems running alchemify resolves the problem.
> Thanks again,
> From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Vermaas, Joshua [Joshua.Vermaas_at_nrel.gov]
> Sent: 25 May 2017 15:29
> To: namd-l_at_ks.uiuc.edu; Jeff Comer
> Subject: Re: namd-l: Error regarding missing angles between perturbed groups for fep calculation
> Hi Gareth,
> In principle this should be taken care of by what used to be alchemify,
> but is now incorporated into NAMD itself. Bond and angle terms that
> might exist between the appearing and disappearing atoms are removed
> prior to checking for parameters. How did you tag your groups? When I
> get these errors, the first thing I check is the pdb tags for the
> appearing and disappearing groups, and usually I just didn't
> appropriately tag what I thought I did.
> On 05/25/2017 03:27 PM, Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES
> SPACE RESEARCH ASSOCIATION] wrote:
>> Hi Jeff,
>> Many thanks for your response. You understand though that NN2 and NN2B should not be able to 'see' each other. As one is annihilated the other is appearing. For this reason I don't see why an angle term needs to be specified.
>> Does this change your point of view?
>> From: Jeff Comer [jeffcomer_at_gmail.com]
>> Sent: 25 May 2017 14:16
>> To: NAMD list; Shannon, Gareth Bayley. (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION]
>> Subject: Re: namd-l: Error regarding missing angles between perturbed groups for fep calculation
>> Hi Gareth,
>> The error means that the parameter files you are including with
>> "parameters" keywords in your NAMD configuration file do not include
>> an angle for the atom types NN2 CN7B NN2B. I'm guessing you are using
>> "par_all36_na.prm". This parameter may be missing because your FEP
>> structure has some unusual bonding topology. You either need to change
>> the topology or determine reasonable values for these parameters.
>> Jeffrey Comer, PhD
>> Assistant Professor
>> Institute of Computational Comparative Medicine
>> Nanotechnology Innovation Center of Kansas State
>> Kansas State University
>> Office: P-213 Mosier Hall
>> Phone: 785-532-6311
>> Website: https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fjeffcomer.us&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C12cb795e2c964e2f621408d4a3b4d6a1%7Ca0f29d7e28cd4f5484427885aee7c080%7C1%7C0%7C636313444475822481&sdata=8tRXZWxzdOzCgIMqLbX0W7%2F2O8BcdF1a5yI5ss2n2l4%3D&reserved=0
>> On Thu, May 25, 2017 at 10:49 AM, Shannon, Gareth Bayley.
>> (ARC-SS)[UNIVERSITIES SPACE RESEARCH ASSOCIATION]
>> <gareth.b.shannon_at_nasa.gov> wrote:
>>> Hello all,
>>> I am trying to do FEP to get the delta G of ATP to GTP in solution.
>>> I am using:
>>> To build the vacuum psf: PSFGEN 1.5.0 from NAMD 2.8
>>> To solvate and add ions: VMD 1.9.2
>>> To perform dynamics: NAMD 2.12
>>> I am still getting an error due to angles being missing between the two
>>> perturbed groups which I understand shouldn't be an issue for the NAMD
>>> version I am using (later than 2.7b2):
>>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR NN2 CN7B NN2B (ATOMS 10 4
>>> The two nitrogen atoms referenced (atoms 10 and 29) above are the equivalent
>>> atoms in the two perturbed groups.
>>> Can anyone advise how to go about solving this problem please?
>>> Many thanks,
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