AMBER Archive (2008)

Subject: RE: AMBER: problem with minimization

From: Ross Walker (
Date: Thu Aug 07 2008 - 10:40:46 CDT

>I have a problem when try to do energy minimization of an average structure of MD trajectory. Here is the error message:
>forrtl: severe (174): SIGSEGV, segmentation fault occurred
>forrtl: severe (174): SIGSEGV, segmentation fault occurred
>rank 1 in job 23 msunmr6_33508 caused collective abort of all ranks
> exit status of rank 1: return code 174
>for the output, it stops at the first step:
> 1 NaN NaN 8.1543E+17 HD22 3787
> BOND = 461855.0703 ANGLE = 197335.8187 DIHED = 8488.8753
> VDWAALS = NaN EEL = NaN HBOND = 0.0000
> 1-4 VDW = ************* 1-4 EEL = 25910.9799 RESTRAINT = 0.0000
>the input file is simple:
> imin=1, maxcyc=2500,
> ncyc=1000, ntb=0,
> ntr=0,
> cut=12,
Here the NaN under energy, RMS, VDWAALS and EEL mean that the energy of these terms in infinite. The *'s in the 1-4 VDW mean that the value is too large to print. This is most likely caused by a division by zero meaning you have two atoms sitting on top of each other. Since this is step 1 of the minimization is implies that there is something very wrong with your initial structure, note the bonds and angle terms are also very large. Did you go through and prune the pdb file of any duplicate conformations? Sometimes pdb's have multiple ligands in them, all on top of each other, or multiple conformations of the same residue and leap may have picked up both of these.

Load the prmtop and inpcrd file into something like VMD and take a close look at everything. In particular look at the area around atom number 3787 (HD22) since this is the one with the highest force on it and so is probable the origin of the problems.

Good luck

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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