Re: [AMBER] Problem with topology file generation

From: Gustavo Seabra via AMBER <amber.ambermd.org>
Date: Sat, 5 Nov 2022 12:45:52 +0000

Hi,

This is unlikely to solve the problem, sorry.

But beyond the parmtop, you probably will be experiencing difficulty in writing the inpcrd file for a system this large. So, I just wanted to point out that, for large systems, it may be helpful to use a command in LEaP that allows building the input directly in NetCDF format. Your last line could be:

`saveAmberParmNetCDF mol model.parm7 model.ncrst`

And the final coordinate file would be OK. I don't know how to solve the parmtop part, though. Sorry. I hope some expert will chime in here.

All the best, 

--
Gustavo Seabra.
________________________________
From: Tanmoy Paul via AMBER <amber.ambermd.org>
Sent: Friday, November 4, 2022 11:19:16 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] Problem with topology file generation
Dear Amber users,
                                I am Tanmoy from Georgia State University.
I am trying to generate topology and inpcrd files for a system that
contains around 400,000 atoms. Upon solvating, the atom number becomes
around 5,000,000. I used tleap to generate topology and inpcrd files. The
leap.log file did not have any error messages. But while loading them to
VMD, I am getting the following error:
*PARM7: error reading bond number 4015670*
Initially, we thought that it was an issue of visualization. But while
trying to run minimization in NAMD we again encountered the same error. We
were able to generate topology and inpcrd files without the solvent and
ions successfully. It was loaded to vmd without any errors or strange
connections. I checked the prmtop to the best of my ability and found a
strange thing. Under the %FLAG BONDS_INC_HYDROGEN, I can see atom numbers
that are larger than the total number of atoms I have (5530618).
16591827     1161659183316591830     1171659183916591836     11616591842
16591836
I do not know how this is even possible. Can anyone please help?
Here is the script we used :
source leaprc.protein.ff14SB
source leaprc.DNA.bsc1
source leaprc.water.tip3p
loadamberparams /usr/local/amber16/dat/leap/parm/frcmod.ionsjc_tip3p
loadamberprep   mg.prep
loadamberparams mg.frcmod
loadoff FeS-nCYS.lib
loadoff CYF.lib
loadamberparams FeS.frcmod
mol = loadpdb model.pdb
desc mol.CYF
desc mol.SF4
bond mol.116.SG mol.761.FE1 #first CYF
bond mol.134.SG mol.761.FE3
bond mol.155.SG mol.761.FE2
bond mol.190.SG mol.761.FE4
bond mol.761.FE1 mol.761.S2
bond mol.761.FE1 mol.761.S3
bond mol.761.FE1 mol.761.S4
bond mol.761.FE2 mol.761.S1
bond mol.761.FE2 mol.761.S3
bond mol.761.FE2 mol.761.S4
bond mol.761.FE3 mol.761.S1
bond mol.761.FE3 mol.761.S2
bond mol.761.FE3 mol.761.S4
bond mol.761.FE4 mol.761.S1
bond mol.761.FE4 mol.761.S2
bond mol.761.FE4 mol.761.S3
solvatebox mol TIP3PBOX 12.0
charge mol
addIonsRand mol Na+ 5660 Cl- 5406
check mol
saveamberparm mol model.prmtop model.inpcrd
quit
--
With regards,
Tanmoy
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Received on Sat Nov 05 2022 - 06:00:03 PDT
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