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source leaprc.ff10
loadamberparams frcmod.ionsjc_tip3p
set default PBradii mbondi2
1vom = loadpdb 1vom-clean.pdb
addions 1vom Na+
saveamberparm 1vom prmtop inpcrd

########### resolve a problem

export AMBERHOME=`pwd`
root@shenzy-pc:/home/shenzy/lib/amber14# ./update_amber –apply leap.patch
export AMBERHOME=`pwd`
./update_amber –apply http://ambermd.org/bugfixes/AmberTools/13.0/cygwin_fix

root@shenzy-pc:/home/shenzy/lib/amber14# cat leap.patch
*******>leap.patch

Author: Jason Swails

Date: 30 April, 2014

Programs: tleap, xleap

Description: Solves potential inpcrd file truncation from tleap

——————————————————————————–

diff –git AmberTools/src/leap/src/leap/unitio.c AmberTools/src/leap/src/leap/unitio.c
index cbab939..4e78ee3 100644
— AmberTools/src/leap/src/leap/unitio.c
+++ AmberTools/src/leap/src/leap/unitio.c
@@ -6897,6 +6897,7 @@ if (bPolar && GDefaults.iIPOL <= 0) // NOT allowed to save IPOL=0 for polarizabl
VarArrayDestroy(&vaExcludedCount);
VarArrayDestroy(&vaNBIndex);
VarArrayDestroy(&vaNonBonds);
+ fclose( fCrd );

}

@@ -8528,6 +8529,7 @@ IX_DESC iResIx;
VarArrayDestroy( &vaExcludedCount );
VarArrayDestroy( &vaNBIndex );
VarArrayDestroy( &vaNonBonds );
+ fclose( fCrd );

}
static char *prepfmt = ” %-3d %-4s %-4s %c %f %f %f %f\n”;

> Thanks for the response. 
> 
> Yes, I am sure that I am using ntb = 0. I also know that it works prior to 
> adding ions, so adding ions is what breaks it. 
> 

​Yikes… Don’t do this ;). If you plan on running with explicit solvent, 
do this off the bat. (pmemd.cuda doesn’t even support vacuum dynamics). 
 The best way to add ions to a system via tleap is actually to add the 
solvent first and then replace random solvent molecules with ions (at least 
IMO — YMMV). So something like this: 

system = loadPDB you_system.pdb 
ions = loadAmberParams frcmod.ionsjc_tip3p 
solvateOct system TIP3PBOX 15.0 
addIonsRand system Na+ 0 
saveAmberParm system your_system.parm7 your_system.rst7 

The first line loads your system. The second loads the ion parameters (as 
Ilyas mentioned, the “ions=” part is optional). The third solvates the 
system with TIP3P waters in a truncated octahedron with at least a 15 
Angstrom buffer around the solute.​ The fourth replaces enough waters with 
sodium ions to neutralize the system. The last saves your topology file. 
(Of course this assumes a default leaprc file, which you mentioned you had.) 


> Interestingly, the last two lines of the inpcrd of the protein only system 
> reads 
> 
> 82.4450000 14.3940000 -13.6870000 81.7180000 15.3700000 -13.4430000 
> 83.6048830 14.5521392 -13.3126966 
> 
> whereas the inpcrd with ions reads 
> 
> 86.3470000 12.2630000 -15.2900000 87.2459461 11.6555756 -15.3950273 
> 86.5023142 13.2275008 -15.7734415 86.1831237 12.5406017 -13.8148107 
> 87.2007​ 


> This does not look correct to me. But it is purely generated by leap. 
> 

​Looks like you got clipped with a bug we recently found (LEaP occasionally 
truncates files​). An update should be posted tomorrow morning (EST in the 
USA) — here is the relevant thread on the mailing list describing the bug 
http://archive.ambermd.org/201404/0532.html (there is a proposed patch 
attached there that you can download and apply if you don’t want to wait). 

Why are there 6 columns in the first place? I’d expect 3 columns * 
> numberOfAtoms rows. Forgive my gromacs inclination, is this the amber way? 
> 

​Yes — this is the amber way. It is the x, y, z coordinates of two atoms. 

​​ 
> (CRD spec states FORMAT(6F12.7), which is again cryptic to me.) 
> 

​This is a Fortran format statement. It indicates that there are at most 6 
Floating point numbers per line, each with 7 decimal points that take up 
exactly 12 characters. Amber is traditionally a Fortran code-base 
(exclusively back in the early days of Amber 3 to 4, although it is FAR 
more diverse now). You can still see strong remnants of this Fortran 
heritage everywhere. 

And in the last one, there is a row with a single column. Is this supposed 
> to happen? 
> 

​No. It’s a bug that should hopefully have a fix posted soon (see above). 
​ 

> 
> Regards, 
> 
> Murat 
> 
> 
> 
> Here is the full(ish) output including the error. : 
> 
> ​[snip] 
> 
> ——————————————————————————– 
> 1. RESOURCE USE: 
> 
> ——————————————————————————– 
> 
> | Flags: 
> 
> | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation 
> At line 842 of file ew_box.F90 (unit = 9, file = ‘inpcrd’) 
> Fortran runtime error: End of file 
> 

​You got hit by the leap bug — the file was truncated.​ 

Hope this helps, 
Jason