This script should get you past the problem you are seeing. You should be able to install it anywhere in your path. I installed it as /opt/pbs/bin/pbs-config for my testing. Remember to make it executable.
#!/bin/sh
#
# Copyright (C) 1994-2016 Altair Engineering, Inc.
# For more information, contact Altair at www.altair.com.
#
# This file is part of the PBS Professional ("PBS Pro") software.
#
# Open Source License Information:
#
# PBS Pro is free software. You can redistribute it and/or modify it under the
# terms of the GNU Affero General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
#
# PBS Pro is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License along
# with this program. If not, see <http://www.gnu.org/licenses/>.
#
# Commercial License Information:
#
# The PBS Pro software is licensed under the terms of the GNU Affero General
# Public License agreement ("AGPL"), except where a separate commercial license
# agreement for PBS Pro version 14 or later has been executed in writing with Altair.
#
# Altair’s dual-license business model allows companies, individuals, and
# organizations to create proprietary derivative works of PBS Pro and distribute
# them - whether embedded or bundled with other software - under a commercial
# license agreement.
#
# Use of Altair’s trademarks, including but not limited to "PBS™",
# "PBS Professional®", and "PBS Pro™" and Altair’s logos is subject to Altair's
# trademark licensing policies.
. ${PBS_CONF_FILE:-/etc/pbs.conf}
case "$1" in
--prefix)
[ -d "$PBS_EXEC" ] || exit 1
echo $PBS_EXEC
;;
--cflags)
[ -d "$PBS_EXEC/include" ] || exit 1
echo "-I$PBS_EXEC/include"
;;
--libs)
libdir="$PBS_EXEC/lib"
[ -d "$libdir" ] || libdir="$PBS_EXEC/lib64"
[ -d "$libdir" ] || exit 1
echo "-L$libdir -lpbs -lpthread -lcrypto"
;;
*)
exit 1
;;
esac